diff --git a/lib/analyze-action.js b/lib/analyze-action.js
index a2fe4e0b0..389d3e56e 100644
--- a/lib/analyze-action.js
+++ b/lib/analyze-action.js
@@ -88525,7 +88525,7 @@ function checkOverlayBaseDatabase(config, logger, warningPrefix) {
   }
   return true;
 }
-async function uploadOverlayBaseDatabaseToCache(codeql, config, logger) {
+async function cleanupAndUploadOverlayBaseDatabaseToCache(codeql, config, logger) {
   const overlayDatabaseMode = config.overlayDatabaseMode;
   if (overlayDatabaseMode !== "overlay-base" /* OverlayBase */) {
     logger.debug(
@@ -91672,7 +91672,7 @@ async function warnIfGoInstalledAfterInit(config, logger) {
 
 // src/database-upload.ts
 var fs13 = __toESM(require("fs"));
-async function uploadDatabases(repositoryNwo, codeql, config, apiDetails, logger) {
+async function cleanupAndUploadDatabases(repositoryNwo, codeql, config, apiDetails, logger) {
   if (getRequiredInput("upload-database") !== "true") {
     logger.debug("Database upload disabled in workflow. Skipping upload.");
     return;
@@ -94053,8 +94053,14 @@ async function run() {
     } else {
       logger.info("Not uploading results");
     }
-    await uploadOverlayBaseDatabaseToCache(codeql, config, logger);
-    await uploadDatabases(repositoryNwo, codeql, config, apiDetails, logger);
+    await cleanupAndUploadOverlayBaseDatabaseToCache(codeql, config, logger);
+    await cleanupAndUploadDatabases(
+      repositoryNwo,
+      codeql,
+      config,
+      apiDetails,
+      logger
+    );
     const trapCacheUploadStartTime = import_perf_hooks3.performance.now();
     didUploadTrapCaches = await uploadTrapCaches(codeql, config, logger);
     trapCacheUploadTime = import_perf_hooks3.performance.now() - trapCacheUploadStartTime;
diff --git a/src/analyze-action.ts b/src/analyze-action.ts
index 3ab1dd132..a101a0187 100644
--- a/src/analyze-action.ts
+++ b/src/analyze-action.ts
@@ -25,7 +25,7 @@ import {
   isCodeQualityEnabled,
   isCodeScanningEnabled,
 } from "./config-utils";
-import { uploadDatabases } from "./database-upload";
+import { cleanupAndUploadDatabases } from "./database-upload";
 import {
   DependencyCacheUploadStatusReport,
   uploadDependencyCaches,
@@ -35,7 +35,7 @@ import { EnvVar } from "./environment";
 import { Feature, Features } from "./feature-flags";
 import { KnownLanguage } from "./languages";
 import { getActionsLogger, Logger } from "./logging";
-import { uploadOverlayBaseDatabaseToCache } from "./overlay-database-utils";
+import { cleanupAndUploadOverlayBaseDatabaseToCache } from "./overlay-database-utils";
 import { getRepositoryNwo } from "./repository";
 import * as statusReport from "./status-report";
 import {
@@ -417,12 +417,20 @@ async function run() {
     }
 
     // Possibly upload the overlay-base database to actions cache.
-    // If databases are to be uploaded, they will first be cleaned up at the overlay level.
-    await uploadOverlayBaseDatabaseToCache(codeql, config, logger);
+    // Note: Take care with the ordering of this call since databases may be cleaned up
+    // at the `overlay` level.
+    await cleanupAndUploadOverlayBaseDatabaseToCache(codeql, config, logger);
 
     // Possibly upload the database bundles for remote queries.
-    // If databases are to be uploaded, they will first be cleaned up at the clear level.
-    await uploadDatabases(repositoryNwo, codeql, config, apiDetails, logger);
+    // Note: Take care with the ordering of this call since databases may be cleaned up
+    // at the `overlay` or `clear` level.
+    await cleanupAndUploadDatabases(
+      repositoryNwo,
+      codeql,
+      config,
+      apiDetails,
+      logger,
+    );
 
     // Possibly upload the TRAP caches for later re-use
     const trapCacheUploadStartTime = performance.now();
diff --git a/src/database-upload.test.ts b/src/database-upload.test.ts
index 6c986fb7f..92f3d75b5 100644
--- a/src/database-upload.test.ts
+++ b/src/database-upload.test.ts
@@ -10,7 +10,7 @@ import { GitHubApiDetails } from "./api-client";
 import * as apiClient from "./api-client";
 import { createStubCodeQL } from "./codeql";
 import { Config } from "./config-utils";
-import { uploadDatabases } from "./database-upload";
+import { cleanupAndUploadDatabases } from "./database-upload";
 import * as gitUtils from "./git-utils";
 import { KnownLanguage } from "./languages";
 import { RepositoryNwo } from "./repository";
@@ -91,7 +91,7 @@ test("Abort database upload if 'upload-database' input set to false", async (t)
     sinon.stub(gitUtils, "isAnalyzingDefaultBranch").resolves(true);
 
     const loggedMessages = [];
-    await uploadDatabases(
+    await cleanupAndUploadDatabases(
       testRepoName,
       getCodeQL(),
       getTestConfig(tmpDir),
@@ -121,7 +121,7 @@ test("Abort database upload if 'analysis-kinds: code-scanning' is not enabled",
     await mockHttpRequests(201);
 
     const loggedMessages = [];
-    await uploadDatabases(
+    await cleanupAndUploadDatabases(
       testRepoName,
       getCodeQL(),
       {
@@ -155,7 +155,7 @@ test("Abort database upload if running against GHES", async (t) => {
     config.gitHubVersion = { type: GitHubVariant.GHES, version: "3.0" };
 
     const loggedMessages = [];
-    await uploadDatabases(
+    await cleanupAndUploadDatabases(
       testRepoName,
       getCodeQL(),
       config,
@@ -183,7 +183,7 @@ test("Abort database upload if not analyzing default branch", async (t) => {
     sinon.stub(gitUtils, "isAnalyzingDefaultBranch").resolves(false);
 
     const loggedMessages = [];
-    await uploadDatabases(
+    await cleanupAndUploadDatabases(
       testRepoName,
       getCodeQL(),
       getTestConfig(tmpDir),
@@ -212,7 +212,7 @@ test("Don't crash if uploading a database fails", async (t) => {
     await mockHttpRequests(500);
 
     const loggedMessages = [] as LoggedMessage[];
-    await uploadDatabases(
+    await cleanupAndUploadDatabases(
       testRepoName,
       getCodeQL(),
       getTestConfig(tmpDir),
@@ -243,7 +243,7 @@ test("Successfully uploading a database to github.com", async (t) => {
     await mockHttpRequests(201);
 
     const loggedMessages = [] as LoggedMessage[];
-    await uploadDatabases(
+    await cleanupAndUploadDatabases(
       testRepoName,
       getCodeQL(),
       getTestConfig(tmpDir),
@@ -272,7 +272,7 @@ test("Successfully uploading a database to GHEC-DR", async (t) => {
     const databaseUploadSpy = await mockHttpRequests(201);
 
     const loggedMessages = [] as LoggedMessage[];
-    await uploadDatabases(
+    await cleanupAndUploadDatabases(
       testRepoName,
       getCodeQL(),
       getTestConfig(tmpDir),
diff --git a/src/database-upload.ts b/src/database-upload.ts
index 69175178c..7a147fbc7 100644
--- a/src/database-upload.ts
+++ b/src/database-upload.ts
@@ -11,7 +11,7 @@ import { RepositoryNwo } from "./repository";
 import * as util from "./util";
 import { bundleDb, parseGitHubUrl } from "./util";
 
-export async function uploadDatabases(
+export async function cleanupAndUploadDatabases(
   repositoryNwo: RepositoryNwo,
   codeql: CodeQL,
   config: Config,
diff --git a/src/overlay-database-utils.ts b/src/overlay-database-utils.ts
index ebb020ba8..5b0b4643d 100644
--- a/src/overlay-database-utils.ts
+++ b/src/overlay-database-utils.ts
@@ -204,7 +204,7 @@ export function checkOverlayBaseDatabase(
  * @returns A promise that resolves to true if the upload was performed and
  * successfully completed, or false otherwise
  */
-export async function uploadOverlayBaseDatabaseToCache(
+export async function cleanupAndUploadOverlayBaseDatabaseToCache(
   codeql: CodeQL,
   config: Config,
   logger: Logger,