diff --git a/.github/workflows/__export-file-baseline-information.yml b/.github/workflows/__export-file-baseline-information.yml
index f157c23f7..41fb9220f 100644
--- a/.github/workflows/__export-file-baseline-information.yml
+++ b/.github/workflows/__export-file-baseline-information.yml
@@ -125,5 +125,6 @@ jobs:
             fi
           done
     env:
+      CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS: false
       CODEQL_ACTION_SUBLANGUAGE_FILE_COVERAGE: true
       CODEQL_ACTION_TEST_MODE: true
diff --git a/lib/analyze-action-post.js b/lib/analyze-action-post.js
index c202c7219..647a56f9f 100644
--- a/lib/analyze-action-post.js
+++ b/lib/analyze-action-post.js
@@ -127971,6 +127971,15 @@ var featureConfig = {
     legacyApi: true,
     minimumVersion: void 0
   },
+  ["skip_file_coverage_on_prs" /* SkipFileCoverageOnPrs */]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS",
+    // For testing, this is not behind a CLI version check yet. However
+    // before rolling this out externally, we should set a minimum version here
+    // since current versions of the CodeQL CLI will log if baseline information
+    // cannot be found when interpreting results.
+    minimumVersion: void 0
+  },
   ["upload_overlay_db_to_api" /* UploadOverlayDbToApi */]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_UPLOAD_OVERLAY_DB_TO_API",
@@ -128188,6 +128197,10 @@ async function getCodeQLForCmd(cmd, checkVersion) {
       } else if (overlayDatabaseMode === "overlay-base" /* OverlayBase */) {
         extraArgs.push("--overlay-base");
       }
+      const baselineFilesOptions = config.enableFileCoverageInformation ? [
+        "--calculate-language-specific-baseline",
+        "--sublanguage-file-coverage"
+      ] : ["--no-calculate-baseline"];
       await runCli(
         cmd,
         [
@@ -128197,12 +128210,14 @@ async function getCodeQLForCmd(cmd, checkVersion) {
           "--db-cluster",
           config.dbLocation,
           `--source-root=${sourceRoot}`,
-          "--calculate-language-specific-baseline",
+          ...baselineFilesOptions,
           "--extractor-include-aliases",
-          "--sublanguage-file-coverage",
           ...extraArgs,
           ...getExtraOptionsFromEnv(["database", "init"], {
-            ignoringOptions: ["--overwrite"]
+            // Some user configs specify `--no-calculate-baseline` as an additional
+            // argument to `codeql database init`. Therefore ignore the baseline file
+            // options here to avoid specifying the same argument twice and erroring.
+            ignoringOptions: ["--overwrite", ...baselineFilesOptions]
           })
         ],
         { stdin: externalRepositoryToken }
@@ -128389,15 +128404,6 @@ ${output}`
         noStreamStdout: true
       });
     },
-    async databasePrintBaseline(databasePath) {
-      const codeqlArgs = [
-        "database",
-        "print-baseline",
-        ...getExtraOptionsFromEnv(["database", "print-baseline"]),
-        databasePath
-      ];
-      return await runCli(cmd, codeqlArgs);
-    },
     async databaseCleanupCluster(config, cleanupLevel) {
       const cacheCleanupFlag = await codeQlVersionAtLeast(
         this,
diff --git a/lib/analyze-action.js b/lib/analyze-action.js
index f97210922..0ab72d31c 100644
--- a/lib/analyze-action.js
+++ b/lib/analyze-action.js
@@ -90723,6 +90723,15 @@ var featureConfig = {
     legacyApi: true,
     minimumVersion: void 0
   },
+  ["skip_file_coverage_on_prs" /* SkipFileCoverageOnPrs */]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS",
+    // For testing, this is not behind a CLI version check yet. However
+    // before rolling this out externally, we should set a minimum version here
+    // since current versions of the CodeQL CLI will log if baseline information
+    // cannot be found when interpreting results.
+    minimumVersion: void 0
+  },
   ["upload_overlay_db_to_api" /* UploadOverlayDbToApi */]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_UPLOAD_OVERLAY_DB_TO_API",
@@ -92482,6 +92491,10 @@ async function getCodeQLForCmd(cmd, checkVersion) {
       } else if (overlayDatabaseMode === "overlay-base" /* OverlayBase */) {
         extraArgs.push("--overlay-base");
       }
+      const baselineFilesOptions = config.enableFileCoverageInformation ? [
+        "--calculate-language-specific-baseline",
+        "--sublanguage-file-coverage"
+      ] : ["--no-calculate-baseline"];
       await runCli(
         cmd,
         [
@@ -92491,12 +92504,14 @@ async function getCodeQLForCmd(cmd, checkVersion) {
           "--db-cluster",
           config.dbLocation,
           `--source-root=${sourceRoot}`,
-          "--calculate-language-specific-baseline",
+          ...baselineFilesOptions,
           "--extractor-include-aliases",
-          "--sublanguage-file-coverage",
           ...extraArgs,
           ...getExtraOptionsFromEnv(["database", "init"], {
-            ignoringOptions: ["--overwrite"]
+            // Some user configs specify `--no-calculate-baseline` as an additional
+            // argument to `codeql database init`. Therefore ignore the baseline file
+            // options here to avoid specifying the same argument twice and erroring.
+            ignoringOptions: ["--overwrite", ...baselineFilesOptions]
           })
         ],
         { stdin: externalRepositoryToken }
@@ -92683,15 +92698,6 @@ ${output}`
         noStreamStdout: true
       });
     },
-    async databasePrintBaseline(databasePath) {
-      const codeqlArgs = [
-        "database",
-        "print-baseline",
-        ...getExtraOptionsFromEnv(["database", "print-baseline"]),
-        databasePath
-      ];
-      return await runCli(cmd, codeqlArgs);
-    },
     async databaseCleanupCluster(config, cleanupLevel) {
       const cacheCleanupFlag = await codeQlVersionAtLeast(
         this,
@@ -93447,10 +93453,17 @@ async function runQueries(sarifFolder, memoryFlag, threadsFlag, diffRangePackDir
       const endTimeInterpretResults = /* @__PURE__ */ new Date();
       statusReport[`interpret_results_${language}_duration_ms`] = endTimeInterpretResults.getTime() - startTimeInterpretResults.getTime();
       logger.endGroup();
-      logger.info(analysisSummary);
-      if (qualityAnalysisSummary) {
+      if (analysisSummary.trim()) {
+        logger.info(analysisSummary);
+      }
+      if (qualityAnalysisSummary?.trim()) {
         logger.info(qualityAnalysisSummary);
       }
+      if (!config.enableFileCoverageInformation) {
+        logger.info(
+          "To speed up pull request analysis, file coverage information is only enabled when analyzing the default branch and protected branches."
+        );
+      }
       if (await features.getValue("qa_telemetry_enabled" /* QaTelemetryEnabled */)) {
         const perQueryAlertCounts = getPerQueryAlertCounts(sarifFile);
         const perQueryAlertCountEventReport = {
diff --git a/lib/autobuild-action.js b/lib/autobuild-action.js
index 6d8e945cf..0a73443cb 100644
--- a/lib/autobuild-action.js
+++ b/lib/autobuild-action.js
@@ -87056,6 +87056,15 @@ var featureConfig = {
     legacyApi: true,
     minimumVersion: void 0
   },
+  ["skip_file_coverage_on_prs" /* SkipFileCoverageOnPrs */]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS",
+    // For testing, this is not behind a CLI version check yet. However
+    // before rolling this out externally, we should set a minimum version here
+    // since current versions of the CodeQL CLI will log if baseline information
+    // cannot be found when interpreting results.
+    minimumVersion: void 0
+  },
   ["upload_overlay_db_to_api" /* UploadOverlayDbToApi */]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_UPLOAD_OVERLAY_DB_TO_API",
@@ -87582,6 +87591,10 @@ async function getCodeQLForCmd(cmd, checkVersion) {
       } else if (overlayDatabaseMode === "overlay-base" /* OverlayBase */) {
         extraArgs.push("--overlay-base");
       }
+      const baselineFilesOptions = config.enableFileCoverageInformation ? [
+        "--calculate-language-specific-baseline",
+        "--sublanguage-file-coverage"
+      ] : ["--no-calculate-baseline"];
       await runCli(
         cmd,
         [
@@ -87591,12 +87604,14 @@ async function getCodeQLForCmd(cmd, checkVersion) {
           "--db-cluster",
           config.dbLocation,
           `--source-root=${sourceRoot}`,
-          "--calculate-language-specific-baseline",
+          ...baselineFilesOptions,
           "--extractor-include-aliases",
-          "--sublanguage-file-coverage",
           ...extraArgs,
           ...getExtraOptionsFromEnv(["database", "init"], {
-            ignoringOptions: ["--overwrite"]
+            // Some user configs specify `--no-calculate-baseline` as an additional
+            // argument to `codeql database init`. Therefore ignore the baseline file
+            // options here to avoid specifying the same argument twice and erroring.
+            ignoringOptions: ["--overwrite", ...baselineFilesOptions]
           })
         ],
         { stdin: externalRepositoryToken }
@@ -87783,15 +87798,6 @@ ${output}`
         noStreamStdout: true
       });
     },
-    async databasePrintBaseline(databasePath) {
-      const codeqlArgs = [
-        "database",
-        "print-baseline",
-        ...getExtraOptionsFromEnv(["database", "print-baseline"]),
-        databasePath
-      ];
-      return await runCli(cmd, codeqlArgs);
-    },
     async databaseCleanupCluster(config, cleanupLevel) {
       const cacheCleanupFlag = await codeQlVersionAtLeast(
         this,
diff --git a/lib/init-action-post.js b/lib/init-action-post.js
index 93d7288a8..0ed7f239d 100644
--- a/lib/init-action-post.js
+++ b/lib/init-action-post.js
@@ -131365,6 +131365,15 @@ var featureConfig = {
     legacyApi: true,
     minimumVersion: void 0
   },
+  ["skip_file_coverage_on_prs" /* SkipFileCoverageOnPrs */]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS",
+    // For testing, this is not behind a CLI version check yet. However
+    // before rolling this out externally, we should set a minimum version here
+    // since current versions of the CodeQL CLI will log if baseline information
+    // cannot be found when interpreting results.
+    minimumVersion: void 0
+  },
   ["upload_overlay_db_to_api" /* UploadOverlayDbToApi */]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_UPLOAD_OVERLAY_DB_TO_API",
@@ -132827,6 +132836,10 @@ async function getCodeQLForCmd(cmd, checkVersion) {
       } else if (overlayDatabaseMode === "overlay-base" /* OverlayBase */) {
         extraArgs.push("--overlay-base");
       }
+      const baselineFilesOptions = config.enableFileCoverageInformation ? [
+        "--calculate-language-specific-baseline",
+        "--sublanguage-file-coverage"
+      ] : ["--no-calculate-baseline"];
       await runCli(
         cmd,
         [
@@ -132836,12 +132849,14 @@ async function getCodeQLForCmd(cmd, checkVersion) {
           "--db-cluster",
           config.dbLocation,
           `--source-root=${sourceRoot}`,
-          "--calculate-language-specific-baseline",
+          ...baselineFilesOptions,
           "--extractor-include-aliases",
-          "--sublanguage-file-coverage",
           ...extraArgs,
           ...getExtraOptionsFromEnv(["database", "init"], {
-            ignoringOptions: ["--overwrite"]
+            // Some user configs specify `--no-calculate-baseline` as an additional
+            // argument to `codeql database init`. Therefore ignore the baseline file
+            // options here to avoid specifying the same argument twice and erroring.
+            ignoringOptions: ["--overwrite", ...baselineFilesOptions]
           })
         ],
         { stdin: externalRepositoryToken }
@@ -133028,15 +133043,6 @@ ${output}`
         noStreamStdout: true
       });
     },
-    async databasePrintBaseline(databasePath) {
-      const codeqlArgs = [
-        "database",
-        "print-baseline",
-        ...getExtraOptionsFromEnv(["database", "print-baseline"]),
-        databasePath
-      ];
-      return await runCli(cmd, codeqlArgs);
-    },
     async databaseCleanupCluster(config, cleanupLevel) {
       const cacheCleanupFlag = await codeQlVersionAtLeast(
         this,
diff --git a/lib/init-action.js b/lib/init-action.js
index cd8d128dd..ee50500d7 100644
--- a/lib/init-action.js
+++ b/lib/init-action.js
@@ -88214,6 +88214,15 @@ var featureConfig = {
     legacyApi: true,
     minimumVersion: void 0
   },
+  ["skip_file_coverage_on_prs" /* SkipFileCoverageOnPrs */]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS",
+    // For testing, this is not behind a CLI version check yet. However
+    // before rolling this out externally, we should set a minimum version here
+    // since current versions of the CodeQL CLI will log if baseline information
+    // cannot be found when interpreting results.
+    minimumVersion: void 0
+  },
   ["upload_overlay_db_to_api" /* UploadOverlayDbToApi */]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_UPLOAD_OVERLAY_DB_TO_API",
@@ -88773,7 +88782,8 @@ async function initActionState({
   features,
   repositoryProperties,
   analysisKinds,
-  logger
+  logger,
+  enableFileCoverageInformation
 }, userConfig) {
   const languages = await getLanguages(
     codeql,
@@ -88835,7 +88845,8 @@ async function initActionState({
     extraQueryExclusions: [],
     overlayDatabaseMode: "none" /* None */,
     useOverlayDatabaseCaching: false,
-    repositoryProperties
+    repositoryProperties,
+    enableFileCoverageInformation
   };
 }
 async function downloadCacheWithTime(trapCachingEnabled, codeQL, languages, logger) {
@@ -90830,6 +90841,10 @@ async function getCodeQLForCmd(cmd, checkVersion) {
       } else if (overlayDatabaseMode === "overlay-base" /* OverlayBase */) {
         extraArgs.push("--overlay-base");
       }
+      const baselineFilesOptions = config.enableFileCoverageInformation ? [
+        "--calculate-language-specific-baseline",
+        "--sublanguage-file-coverage"
+      ] : ["--no-calculate-baseline"];
       await runCli(
         cmd,
         [
@@ -90839,12 +90854,14 @@ async function getCodeQLForCmd(cmd, checkVersion) {
           "--db-cluster",
           config.dbLocation,
           `--source-root=${sourceRoot}`,
-          "--calculate-language-specific-baseline",
+          ...baselineFilesOptions,
           "--extractor-include-aliases",
-          "--sublanguage-file-coverage",
           ...extraArgs,
           ...getExtraOptionsFromEnv(["database", "init"], {
-            ignoringOptions: ["--overwrite"]
+            // Some user configs specify `--no-calculate-baseline` as an additional
+            // argument to `codeql database init`. Therefore ignore the baseline file
+            // options here to avoid specifying the same argument twice and erroring.
+            ignoringOptions: ["--overwrite", ...baselineFilesOptions]
           })
         ],
         { stdin: externalRepositoryToken }
@@ -91031,15 +91048,6 @@ ${output}`
         noStreamStdout: true
       });
     },
-    async databasePrintBaseline(databasePath) {
-      const codeqlArgs = [
-        "database",
-        "print-baseline",
-        ...getExtraOptionsFromEnv(["database", "print-baseline"]),
-        databasePath
-      ];
-      return await runCli(cmd, codeqlArgs);
-    },
     async databaseCleanupCluster(config, cleanupLevel) {
       const cacheCleanupFlag = await codeQlVersionAtLeast(
         this,
@@ -91461,6 +91469,16 @@ function cleanupDatabaseClusterDirectory(config, logger, options = {}, rmSync2 =
     }
   }
 }
+async function getFileCoverageInformationEnabled(debugMode, repositoryNwo, features) {
+  return (
+    // Always enable file coverage information in debug mode
+    debugMode || // We're most interested in speeding up PRs, and we want to keep
+    // submitting file coverage information for the default branch since
+    // it is used to populate the status page.
+    !isAnalyzingPullRequest() || // For now, restrict this feature to the GitHub org
+    repositoryNwo.owner !== "github" || !await features.getValue("skip_file_coverage_on_prs" /* SkipFileCoverageOnPrs */)
+  );
+}
 
 // src/status-report.ts
 var os5 = __toESM(require("os"));
@@ -92067,6 +92085,7 @@ async function run(startedAt) {
       }
     }
     analysisKinds = await getAnalysisKinds(logger);
+    const debugMode = getOptionalInput("debug") === "true" || core13.isDebug();
     config = await initConfig2(features, {
       analysisKinds,
       languagesInput: getOptionalInput("languages"),
@@ -92083,7 +92102,7 @@ async function run(startedAt) {
       // - The `init` Action is passed `debug: true`.
       // - Actions step debugging is enabled (e.g. by [enabling debug logging for a rerun](https://docs.github.com/en/actions/managing-workflow-runs/re-running-workflows-and-jobs#re-running-all-the-jobs-in-a-workflow),
       //   or by setting the `ACTIONS_STEP_DEBUG` secret to `true`).
-      debugMode: getOptionalInput("debug") === "true" || core13.isDebug(),
+      debugMode,
       debugArtifactName: getOptionalInput("debug-artifact-name") || DEFAULT_DEBUG_ARTIFACT_NAME,
       debugDatabaseName: getOptionalInput("debug-database-name") || DEFAULT_DEBUG_DATABASE_NAME,
       repository: repositoryNwo,
@@ -92095,6 +92114,11 @@ async function run(startedAt) {
       apiDetails,
       features,
       repositoryProperties,
+      enableFileCoverageInformation: await getFileCoverageInformationEnabled(
+        debugMode,
+        repositoryNwo,
+        features
+      ),
       logger
     });
     await checkInstallPython311(config.languages, codeql);
diff --git a/lib/resolve-environment-action.js b/lib/resolve-environment-action.js
index 9e5018d61..cc6aa521c 100644
--- a/lib/resolve-environment-action.js
+++ b/lib/resolve-environment-action.js
@@ -87047,6 +87047,15 @@ var featureConfig = {
     legacyApi: true,
     minimumVersion: void 0
   },
+  ["skip_file_coverage_on_prs" /* SkipFileCoverageOnPrs */]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS",
+    // For testing, this is not behind a CLI version check yet. However
+    // before rolling this out externally, we should set a minimum version here
+    // since current versions of the CodeQL CLI will log if baseline information
+    // cannot be found when interpreting results.
+    minimumVersion: void 0
+  },
   ["upload_overlay_db_to_api" /* UploadOverlayDbToApi */]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_UPLOAD_OVERLAY_DB_TO_API",
@@ -87270,6 +87279,10 @@ async function getCodeQLForCmd(cmd, checkVersion) {
       } else if (overlayDatabaseMode === "overlay-base" /* OverlayBase */) {
         extraArgs.push("--overlay-base");
       }
+      const baselineFilesOptions = config.enableFileCoverageInformation ? [
+        "--calculate-language-specific-baseline",
+        "--sublanguage-file-coverage"
+      ] : ["--no-calculate-baseline"];
       await runCli(
         cmd,
         [
@@ -87279,12 +87292,14 @@ async function getCodeQLForCmd(cmd, checkVersion) {
           "--db-cluster",
           config.dbLocation,
           `--source-root=${sourceRoot}`,
-          "--calculate-language-specific-baseline",
+          ...baselineFilesOptions,
           "--extractor-include-aliases",
-          "--sublanguage-file-coverage",
           ...extraArgs,
           ...getExtraOptionsFromEnv(["database", "init"], {
-            ignoringOptions: ["--overwrite"]
+            // Some user configs specify `--no-calculate-baseline` as an additional
+            // argument to `codeql database init`. Therefore ignore the baseline file
+            // options here to avoid specifying the same argument twice and erroring.
+            ignoringOptions: ["--overwrite", ...baselineFilesOptions]
           })
         ],
         { stdin: externalRepositoryToken }
@@ -87471,15 +87486,6 @@ ${output}`
         noStreamStdout: true
       });
     },
-    async databasePrintBaseline(databasePath) {
-      const codeqlArgs = [
-        "database",
-        "print-baseline",
-        ...getExtraOptionsFromEnv(["database", "print-baseline"]),
-        databasePath
-      ];
-      return await runCli(cmd, codeqlArgs);
-    },
     async databaseCleanupCluster(config, cleanupLevel) {
       const cacheCleanupFlag = await codeQlVersionAtLeast(
         this,
diff --git a/lib/setup-codeql-action.js b/lib/setup-codeql-action.js
index ce8242cc6..7182336ae 100644
--- a/lib/setup-codeql-action.js
+++ b/lib/setup-codeql-action.js
@@ -86957,6 +86957,15 @@ var featureConfig = {
     legacyApi: true,
     minimumVersion: void 0
   },
+  ["skip_file_coverage_on_prs" /* SkipFileCoverageOnPrs */]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS",
+    // For testing, this is not behind a CLI version check yet. However
+    // before rolling this out externally, we should set a minimum version here
+    // since current versions of the CodeQL CLI will log if baseline information
+    // cannot be found when interpreting results.
+    minimumVersion: void 0
+  },
   ["upload_overlay_db_to_api" /* UploadOverlayDbToApi */]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_UPLOAD_OVERLAY_DB_TO_API",
@@ -88584,6 +88593,10 @@ async function getCodeQLForCmd(cmd, checkVersion) {
       } else if (overlayDatabaseMode === "overlay-base" /* OverlayBase */) {
         extraArgs.push("--overlay-base");
       }
+      const baselineFilesOptions = config.enableFileCoverageInformation ? [
+        "--calculate-language-specific-baseline",
+        "--sublanguage-file-coverage"
+      ] : ["--no-calculate-baseline"];
       await runCli(
         cmd,
         [
@@ -88593,12 +88606,14 @@ async function getCodeQLForCmd(cmd, checkVersion) {
           "--db-cluster",
           config.dbLocation,
           `--source-root=${sourceRoot}`,
-          "--calculate-language-specific-baseline",
+          ...baselineFilesOptions,
           "--extractor-include-aliases",
-          "--sublanguage-file-coverage",
           ...extraArgs,
           ...getExtraOptionsFromEnv(["database", "init"], {
-            ignoringOptions: ["--overwrite"]
+            // Some user configs specify `--no-calculate-baseline` as an additional
+            // argument to `codeql database init`. Therefore ignore the baseline file
+            // options here to avoid specifying the same argument twice and erroring.
+            ignoringOptions: ["--overwrite", ...baselineFilesOptions]
           })
         ],
         { stdin: externalRepositoryToken }
@@ -88785,15 +88800,6 @@ ${output}`
         noStreamStdout: true
       });
     },
-    async databasePrintBaseline(databasePath) {
-      const codeqlArgs = [
-        "database",
-        "print-baseline",
-        ...getExtraOptionsFromEnv(["database", "print-baseline"]),
-        databasePath
-      ];
-      return await runCli(cmd, codeqlArgs);
-    },
     async databaseCleanupCluster(config, cleanupLevel) {
       const cacheCleanupFlag = await codeQlVersionAtLeast(
         this,
diff --git a/lib/start-proxy-action-post.js b/lib/start-proxy-action-post.js
index f8e266535..8e31348ce 100644
--- a/lib/start-proxy-action-post.js
+++ b/lib/start-proxy-action-post.js
@@ -127377,6 +127377,15 @@ var featureConfig = {
     legacyApi: true,
     minimumVersion: void 0
   },
+  ["skip_file_coverage_on_prs" /* SkipFileCoverageOnPrs */]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS",
+    // For testing, this is not behind a CLI version check yet. However
+    // before rolling this out externally, we should set a minimum version here
+    // since current versions of the CodeQL CLI will log if baseline information
+    // cannot be found when interpreting results.
+    minimumVersion: void 0
+  },
   ["upload_overlay_db_to_api" /* UploadOverlayDbToApi */]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_UPLOAD_OVERLAY_DB_TO_API",
diff --git a/lib/start-proxy-action.js b/lib/start-proxy-action.js
index e0aca4c39..ea6f8c96c 100644
--- a/lib/start-proxy-action.js
+++ b/lib/start-proxy-action.js
@@ -103926,6 +103926,15 @@ var featureConfig = {
     legacyApi: true,
     minimumVersion: void 0
   },
+  ["skip_file_coverage_on_prs" /* SkipFileCoverageOnPrs */]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS",
+    // For testing, this is not behind a CLI version check yet. However
+    // before rolling this out externally, we should set a minimum version here
+    // since current versions of the CodeQL CLI will log if baseline information
+    // cannot be found when interpreting results.
+    minimumVersion: void 0
+  },
   ["upload_overlay_db_to_api" /* UploadOverlayDbToApi */]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_UPLOAD_OVERLAY_DB_TO_API",
diff --git a/lib/upload-lib.js b/lib/upload-lib.js
index b06c31d8b..7f19a1a08 100644
--- a/lib/upload-lib.js
+++ b/lib/upload-lib.js
@@ -90116,6 +90116,15 @@ var featureConfig = {
     legacyApi: true,
     minimumVersion: void 0
   },
+  ["skip_file_coverage_on_prs" /* SkipFileCoverageOnPrs */]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS",
+    // For testing, this is not behind a CLI version check yet. However
+    // before rolling this out externally, we should set a minimum version here
+    // since current versions of the CodeQL CLI will log if baseline information
+    // cannot be found when interpreting results.
+    minimumVersion: void 0
+  },
   ["upload_overlay_db_to_api" /* UploadOverlayDbToApi */]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_UPLOAD_OVERLAY_DB_TO_API",
@@ -91299,6 +91308,10 @@ async function getCodeQLForCmd(cmd, checkVersion) {
       } else if (overlayDatabaseMode === "overlay-base" /* OverlayBase */) {
         extraArgs.push("--overlay-base");
       }
+      const baselineFilesOptions = config.enableFileCoverageInformation ? [
+        "--calculate-language-specific-baseline",
+        "--sublanguage-file-coverage"
+      ] : ["--no-calculate-baseline"];
       await runCli(
         cmd,
         [
@@ -91308,12 +91321,14 @@ async function getCodeQLForCmd(cmd, checkVersion) {
           "--db-cluster",
           config.dbLocation,
           `--source-root=${sourceRoot}`,
-          "--calculate-language-specific-baseline",
+          ...baselineFilesOptions,
           "--extractor-include-aliases",
-          "--sublanguage-file-coverage",
           ...extraArgs,
           ...getExtraOptionsFromEnv(["database", "init"], {
-            ignoringOptions: ["--overwrite"]
+            // Some user configs specify `--no-calculate-baseline` as an additional
+            // argument to `codeql database init`. Therefore ignore the baseline file
+            // options here to avoid specifying the same argument twice and erroring.
+            ignoringOptions: ["--overwrite", ...baselineFilesOptions]
           })
         ],
         { stdin: externalRepositoryToken }
@@ -91500,15 +91515,6 @@ ${output}`
         noStreamStdout: true
       });
     },
-    async databasePrintBaseline(databasePath) {
-      const codeqlArgs = [
-        "database",
-        "print-baseline",
-        ...getExtraOptionsFromEnv(["database", "print-baseline"]),
-        databasePath
-      ];
-      return await runCli(cmd, codeqlArgs);
-    },
     async databaseCleanupCluster(config, cleanupLevel) {
       const cacheCleanupFlag = await codeQlVersionAtLeast(
         this,
diff --git a/lib/upload-sarif-action-post.js b/lib/upload-sarif-action-post.js
index 8b9c43a98..19eb00c41 100644
--- a/lib/upload-sarif-action-post.js
+++ b/lib/upload-sarif-action-post.js
@@ -127539,6 +127539,15 @@ var featureConfig = {
     legacyApi: true,
     minimumVersion: void 0
   },
+  ["skip_file_coverage_on_prs" /* SkipFileCoverageOnPrs */]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS",
+    // For testing, this is not behind a CLI version check yet. However
+    // before rolling this out externally, we should set a minimum version here
+    // since current versions of the CodeQL CLI will log if baseline information
+    // cannot be found when interpreting results.
+    minimumVersion: void 0
+  },
   ["upload_overlay_db_to_api" /* UploadOverlayDbToApi */]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_UPLOAD_OVERLAY_DB_TO_API",
diff --git a/lib/upload-sarif-action.js b/lib/upload-sarif-action.js
index 2c91f2c97..4b775f252 100644
--- a/lib/upload-sarif-action.js
+++ b/lib/upload-sarif-action.js
@@ -89911,6 +89911,15 @@ var featureConfig = {
     legacyApi: true,
     minimumVersion: void 0
   },
+  ["skip_file_coverage_on_prs" /* SkipFileCoverageOnPrs */]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS",
+    // For testing, this is not behind a CLI version check yet. However
+    // before rolling this out externally, we should set a minimum version here
+    // since current versions of the CodeQL CLI will log if baseline information
+    // cannot be found when interpreting results.
+    minimumVersion: void 0
+  },
   ["upload_overlay_db_to_api" /* UploadOverlayDbToApi */]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_UPLOAD_OVERLAY_DB_TO_API",
@@ -91854,6 +91863,10 @@ async function getCodeQLForCmd(cmd, checkVersion) {
       } else if (overlayDatabaseMode === "overlay-base" /* OverlayBase */) {
         extraArgs.push("--overlay-base");
       }
+      const baselineFilesOptions = config.enableFileCoverageInformation ? [
+        "--calculate-language-specific-baseline",
+        "--sublanguage-file-coverage"
+      ] : ["--no-calculate-baseline"];
       await runCli(
         cmd,
         [
@@ -91863,12 +91876,14 @@ async function getCodeQLForCmd(cmd, checkVersion) {
           "--db-cluster",
           config.dbLocation,
           `--source-root=${sourceRoot}`,
-          "--calculate-language-specific-baseline",
+          ...baselineFilesOptions,
           "--extractor-include-aliases",
-          "--sublanguage-file-coverage",
           ...extraArgs,
           ...getExtraOptionsFromEnv(["database", "init"], {
-            ignoringOptions: ["--overwrite"]
+            // Some user configs specify `--no-calculate-baseline` as an additional
+            // argument to `codeql database init`. Therefore ignore the baseline file
+            // options here to avoid specifying the same argument twice and erroring.
+            ignoringOptions: ["--overwrite", ...baselineFilesOptions]
           })
         ],
         { stdin: externalRepositoryToken }
@@ -92055,15 +92070,6 @@ ${output}`
         noStreamStdout: true
       });
     },
-    async databasePrintBaseline(databasePath) {
-      const codeqlArgs = [
-        "database",
-        "print-baseline",
-        ...getExtraOptionsFromEnv(["database", "print-baseline"]),
-        databasePath
-      ];
-      return await runCli(cmd, codeqlArgs);
-    },
     async databaseCleanupCluster(config, cleanupLevel) {
       const cacheCleanupFlag = await codeQlVersionAtLeast(
         this,
diff --git a/package-lock.json b/package-lock.json
index 5624de160..68d4da28c 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -3792,9 +3792,9 @@
       }
     },
     "node_modules/caniuse-lite": {
-      "version": "1.0.30001727",
-      "resolved": "https://registry.npmjs.org/caniuse-lite/-/caniuse-lite-1.0.30001727.tgz",
-      "integrity": "sha512-pB68nIHmbN6L/4C6MH1DokyR3bYqFwjaSs/sWDHGj4CTcFtQUQMuJftVwWkXq7mNWOybD3KhUv3oWHoGxgP14Q==",
+      "version": "1.0.30001766",
+      "resolved": "https://registry.npmjs.org/caniuse-lite/-/caniuse-lite-1.0.30001766.tgz",
+      "integrity": "sha512-4C0lfJ0/YPjJQHagaE9x2Elb69CIqEPZeG0anQt9SIvIoOH4a4uaRl73IavyO+0qZh6MDLH//DrXThEYKHkmYA==",
       "dev": true,
       "funding": [
         {
@@ -3809,7 +3809,8 @@
           "type": "github",
           "url": "https://github.com/sponsors/ai"
         }
-      ]
+      ],
+      "license": "CC-BY-4.0"
     },
     "node_modules/cbor": {
       "version": "10.0.9",
diff --git a/pr-checks/checks/export-file-baseline-information.yml b/pr-checks/checks/export-file-baseline-information.yml
index fdc352285..e45fc58ca 100644
--- a/pr-checks/checks/export-file-baseline-information.yml
+++ b/pr-checks/checks/export-file-baseline-information.yml
@@ -5,6 +5,7 @@ versions: ["nightly-latest"]
 installGo: true
 installDotNet: true
 env:
+  CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS: false
   CODEQL_ACTION_SUBLANGUAGE_FILE_COVERAGE: true
 steps:
   - uses: ./../action/init
diff --git a/src/analyze.test.ts b/src/analyze.test.ts
index ceabf62ba..27fe4a6f4 100644
--- a/src/analyze.test.ts
+++ b/src/analyze.test.ts
@@ -87,7 +87,6 @@ test("status report fields", async (t) => {
           );
           return "";
         },
-        databasePrintBaseline: async () => "",
       });
 
       const config = createTestConfig({
diff --git a/src/analyze.ts b/src/analyze.ts
index dc631ba98..bb3841504 100644
--- a/src/analyze.ts
+++ b/src/analyze.ts
@@ -495,10 +495,18 @@ export async function runQueries(
         endTimeInterpretResults.getTime() - startTimeInterpretResults.getTime();
       logger.endGroup();
 
-      logger.info(analysisSummary);
-      if (qualityAnalysisSummary) {
+      if (analysisSummary.trim()) {
+        logger.info(analysisSummary);
+      }
+      if (qualityAnalysisSummary?.trim()) {
         logger.info(qualityAnalysisSummary);
       }
+      if (!config.enableFileCoverageInformation) {
+        logger.info(
+          "To speed up pull request analysis, file coverage information is only enabled when analyzing " +
+            "the default branch and protected branches.",
+        );
+      }
 
       if (await features.getValue(Feature.QaTelemetryEnabled)) {
         // Note: QA adds the `code-quality` query suite to the `queries` input,
diff --git a/src/codeql.ts b/src/codeql.ts
index f70e5ffa4..8e7c2bfe2 100644
--- a/src/codeql.ts
+++ b/src/codeql.ts
@@ -186,10 +186,6 @@ export interface CodeQL {
     config: Config,
     features: FeatureEnablement,
   ): Promise<string>;
-  /**
-   * Run 'codeql database print-baseline'.
-   */
-  databasePrintBaseline(databasePath: string): Promise<string>;
   /**
    * Run 'codeql database export-diagnostics'
    *
@@ -493,10 +489,6 @@ export function createStubCodeQL(partialCodeql: Partial<CodeQL>): CodeQL {
       partialCodeql,
       "databaseInterpretResults",
     ),
-    databasePrintBaseline: resolveFunction(
-      partialCodeql,
-      "databasePrintBaseline",
-    ),
     databaseExportDiagnostics: resolveFunction(
       partialCodeql,
       "databaseExportDiagnostics",
@@ -628,6 +620,13 @@ async function getCodeQLForCmd(
         extraArgs.push("--overlay-base");
       }
 
+      const baselineFilesOptions = config.enableFileCoverageInformation
+        ? [
+            "--calculate-language-specific-baseline",
+            "--sublanguage-file-coverage",
+          ]
+        : ["--no-calculate-baseline"];
+
       await runCli(
         cmd,
         [
@@ -639,12 +638,14 @@ async function getCodeQLForCmd(
           "--db-cluster",
           config.dbLocation,
           `--source-root=${sourceRoot}`,
-          "--calculate-language-specific-baseline",
+          ...baselineFilesOptions,
           "--extractor-include-aliases",
-          "--sublanguage-file-coverage",
           ...extraArgs,
           ...getExtraOptionsFromEnv(["database", "init"], {
-            ignoringOptions: ["--overwrite"],
+            // Some user configs specify `--no-calculate-baseline` as an additional
+            // argument to `codeql database init`. Therefore ignore the baseline file
+            // options here to avoid specifying the same argument twice and erroring.
+            ignoringOptions: ["--overwrite", ...baselineFilesOptions],
           }),
         ],
         { stdin: externalRepositoryToken },
@@ -885,15 +886,6 @@ async function getCodeQLForCmd(
         noStreamStdout: true,
       });
     },
-    async databasePrintBaseline(databasePath: string): Promise<string> {
-      const codeqlArgs = [
-        "database",
-        "print-baseline",
-        ...getExtraOptionsFromEnv(["database", "print-baseline"]),
-        databasePath,
-      ];
-      return await runCli(cmd, codeqlArgs);
-    },
     async databaseCleanupCluster(
       config: Config,
       cleanupLevel: CleanupLevel,
diff --git a/src/config-utils.test.ts b/src/config-utils.test.ts
index 337eb85c5..276a7a344 100644
--- a/src/config-utils.test.ts
+++ b/src/config-utils.test.ts
@@ -89,6 +89,7 @@ function createTestInitConfigInputs(
       },
       features: createFeatures([]),
       repositoryProperties: {},
+      enableFileCoverageInformation: true,
       logger: getRunnerLogger(true),
     } satisfies configUtils.InitConfigInputs,
     overrides,
diff --git a/src/config-utils.ts b/src/config-utils.ts
index 772c187b8..a01041899 100644
--- a/src/config-utils.ts
+++ b/src/config-utils.ts
@@ -214,6 +214,11 @@ export interface Config {
    * A partial mapping from repository properties that affect us to their values.
    */
   repositoryProperties: RepositoryProperties;
+
+  /**
+   * Whether to enable file coverage information.
+   */
+  enableFileCoverageInformation: boolean;
 }
 
 async function getSupportedLanguageMap(
@@ -433,6 +438,7 @@ export interface InitConfigInputs {
   apiDetails: api.GitHubApiCombinedDetails;
   features: FeatureEnablement;
   repositoryProperties: RepositoryProperties;
+  enableFileCoverageInformation: boolean;
   analysisKinds: AnalysisKind[];
   logger: Logger;
 }
@@ -462,6 +468,7 @@ export async function initActionState(
     repositoryProperties,
     analysisKinds,
     logger,
+    enableFileCoverageInformation,
   }: InitConfigInputs,
   userConfig: UserConfig,
 ): Promise<Config> {
@@ -542,6 +549,7 @@ export async function initActionState(
     overlayDatabaseMode: OverlayDatabaseMode.None,
     useOverlayDatabaseCaching: false,
     repositoryProperties,
+    enableFileCoverageInformation,
   };
 }
 
diff --git a/src/feature-flags.ts b/src/feature-flags.ts
index 7ad9ecfa4..8de68a28d 100644
--- a/src/feature-flags.ts
+++ b/src/feature-flags.ts
@@ -70,6 +70,8 @@ export enum Feature {
   OverlayAnalysisSwift = "overlay_analysis_swift",
   PythonDefaultIsToNotExtractStdlib = "python_default_is_to_not_extract_stdlib",
   QaTelemetryEnabled = "qa_telemetry_enabled",
+  /** Note that this currently only disables baseline file coverage information. */
+  SkipFileCoverageOnPrs = "skip_file_coverage_on_prs",
   UploadOverlayDbToApi = "upload_overlay_db_to_api",
   UseRepositoryProperties = "use_repository_properties",
   ValidateDbConfig = "validate_db_config",
@@ -286,6 +288,15 @@ export const featureConfig = {
     legacyApi: true,
     minimumVersion: undefined,
   },
+  [Feature.SkipFileCoverageOnPrs]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS",
+    // For testing, this is not behind a CLI version check yet. However
+    // before rolling this out externally, we should set a minimum version here
+    // since current versions of the CodeQL CLI will log if baseline information
+    // cannot be found when interpreting results.
+    minimumVersion: undefined,
+  },
   [Feature.UploadOverlayDbToApi]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_UPLOAD_OVERLAY_DB_TO_API",
diff --git a/src/init-action.ts b/src/init-action.ts
index 8b6c200a0..0d92f46ef 100644
--- a/src/init-action.ts
+++ b/src/init-action.ts
@@ -42,6 +42,7 @@ import {
   checkInstallPython311,
   checkPacksForOverlayCompatibility,
   cleanupDatabaseClusterDirectory,
+  getFileCoverageInformationEnabled,
   initCodeQL,
   initConfig,
   runDatabaseInitCluster,
@@ -334,6 +335,7 @@ async function run(startedAt: Date) {
     }
 
     analysisKinds = await getAnalysisKinds(logger);
+    const debugMode = getOptionalInput("debug") === "true" || core.isDebug();
     config = await initConfig(features, {
       analysisKinds,
       languagesInput: getOptionalInput("languages"),
@@ -350,7 +352,7 @@ async function run(startedAt: Date) {
       // - The `init` Action is passed `debug: true`.
       // - Actions step debugging is enabled (e.g. by [enabling debug logging for a rerun](https://docs.github.com/en/actions/managing-workflow-runs/re-running-workflows-and-jobs#re-running-all-the-jobs-in-a-workflow),
       //   or by setting the `ACTIONS_STEP_DEBUG` secret to `true`).
-      debugMode: getOptionalInput("debug") === "true" || core.isDebug(),
+      debugMode,
       debugArtifactName:
         getOptionalInput("debug-artifact-name") || DEFAULT_DEBUG_ARTIFACT_NAME,
       debugDatabaseName:
@@ -364,6 +366,11 @@ async function run(startedAt: Date) {
       apiDetails,
       features,
       repositoryProperties,
+      enableFileCoverageInformation: await getFileCoverageInformationEnabled(
+        debugMode,
+        repositoryNwo,
+        features,
+      ),
       logger,
     });
 
diff --git a/src/init.test.ts b/src/init.test.ts
index 6640e081f..8106a78f9 100644
--- a/src/init.test.ts
+++ b/src/init.test.ts
@@ -2,14 +2,20 @@ import * as fs from "fs";
 import path from "path";
 
 import test, { ExecutionContext } from "ava";
+import * as sinon from "sinon";
 
+import * as actionsUtil from "./actions-util";
 import { createStubCodeQL } from "./codeql";
+import { Feature } from "./feature-flags";
 import {
   checkPacksForOverlayCompatibility,
   cleanupDatabaseClusterDirectory,
+  getFileCoverageInformationEnabled,
 } from "./init";
 import { KnownLanguage } from "./languages";
+import { parseRepositoryNwo } from "./repository";
 import {
+  createFeatures,
   LoggedMessage,
   createTestConfig,
   getRecordingLogger,
@@ -442,3 +448,61 @@ test(
     expectedResult: true,
   },
 );
+
+test("file coverage information enabled when debugMode is true", async (t) => {
+  t.true(
+    await getFileCoverageInformationEnabled(
+      true, // debugMode
+      parseRepositoryNwo("github/codeql-action"),
+      createFeatures([Feature.SkipFileCoverageOnPrs]),
+    ),
+  );
+});
+
+test("file coverage information enabled when not analyzing a pull request", async (t) => {
+  sinon.stub(actionsUtil, "isAnalyzingPullRequest").returns(false);
+
+  t.true(
+    await getFileCoverageInformationEnabled(
+      false, // debugMode
+      parseRepositoryNwo("github/codeql-action"),
+      createFeatures([Feature.SkipFileCoverageOnPrs]),
+    ),
+  );
+});
+
+test("file coverage information enabled when owner is not 'github'", async (t) => {
+  sinon.stub(actionsUtil, "isAnalyzingPullRequest").returns(true);
+
+  t.true(
+    await getFileCoverageInformationEnabled(
+      false, // debugMode
+      parseRepositoryNwo("other-org/some-repo"),
+      createFeatures([Feature.SkipFileCoverageOnPrs]),
+    ),
+  );
+});
+
+test("file coverage information enabled when feature flag is not enabled", async (t) => {
+  sinon.stub(actionsUtil, "isAnalyzingPullRequest").returns(true);
+
+  t.true(
+    await getFileCoverageInformationEnabled(
+      false, // debugMode
+      parseRepositoryNwo("github/codeql-action"),
+      createFeatures([]),
+    ),
+  );
+});
+
+test("file coverage information disabled when all conditions for skipping are met", async (t) => {
+  sinon.stub(actionsUtil, "isAnalyzingPullRequest").returns(true);
+
+  t.false(
+    await getFileCoverageInformationEnabled(
+      false, // debugMode
+      parseRepositoryNwo("github/codeql-action"),
+      createFeatures([Feature.SkipFileCoverageOnPrs]),
+    ),
+  );
+});
diff --git a/src/init.ts b/src/init.ts
index b399ef8d9..a5c8e9ec0 100644
--- a/src/init.ts
+++ b/src/init.ts
@@ -5,13 +5,22 @@ import * as toolrunner from "@actions/exec/lib/toolrunner";
 import * as io from "@actions/io";
 import * as yaml from "js-yaml";
 
-import { getOptionalInput, isSelfHostedRunner } from "./actions-util";
+import {
+  getOptionalInput,
+  isAnalyzingPullRequest,
+  isSelfHostedRunner,
+} from "./actions-util";
 import { GitHubApiDetails } from "./api-client";
 import { CodeQL, setupCodeQL } from "./codeql";
 import * as configUtils from "./config-utils";
-import { CodeQLDefaultVersionInfo, FeatureEnablement } from "./feature-flags";
+import {
+  CodeQLDefaultVersionInfo,
+  Feature,
+  FeatureEnablement,
+} from "./feature-flags";
 import { KnownLanguage, Language } from "./languages";
 import { Logger, withGroupAsync } from "./logging";
+import { RepositoryNwo } from "./repository";
 import { ToolsSource } from "./setup-codeql";
 import { ZstdAvailability } from "./tar";
 import { ToolsDownloadStatusReport } from "./tools-download";
@@ -288,3 +297,21 @@ export function cleanupDatabaseClusterDirectory(
     }
   }
 }
+
+export async function getFileCoverageInformationEnabled(
+  debugMode: boolean,
+  repositoryNwo: RepositoryNwo,
+  features: FeatureEnablement,
+): Promise<boolean> {
+  return (
+    // Always enable file coverage information in debug mode
+    debugMode ||
+    // We're most interested in speeding up PRs, and we want to keep
+    // submitting file coverage information for the default branch since
+    // it is used to populate the status page.
+    !isAnalyzingPullRequest() ||
+    // For now, restrict this feature to the GitHub org
+    repositoryNwo.owner !== "github" ||
+    !(await features.getValue(Feature.SkipFileCoverageOnPrs))
+  );
+}
diff --git a/src/testing-utils.ts b/src/testing-utils.ts
index bee7d1ada..83ec88ee1 100644
--- a/src/testing-utils.ts
+++ b/src/testing-utils.ts
@@ -408,6 +408,7 @@ export function createTestConfig(overrides: Partial<Config>): Config {
       overlayDatabaseMode: OverlayDatabaseMode.None,
       useOverlayDatabaseCaching: false,
       repositoryProperties: {},
+      enableFileCoverageInformation: true,
     } satisfies Config,
     overrides,
   );