diff --git a/lib/analyze-action-post.js b/lib/analyze-action-post.js
index 7c8823caa..6adbd9db4 100644
--- a/lib/analyze-action-post.js
+++ b/lib/analyze-action-post.js
@@ -161253,6 +161253,18 @@ var core6 = __toESM(require_core());
 // src/config/db-config.ts
 var jsonschema = __toESM(require_lib2());
 var semver2 = __toESM(require_semver2());
+
+// src/feature-flags/properties.ts
+var RepositoryPropertyName = /* @__PURE__ */ ((RepositoryPropertyName2) => {
+  RepositoryPropertyName2["DISABLE_OVERLAY"] = "github-codeql-disable-overlay";
+  RepositoryPropertyName2["EXTRA_QUERIES"] = "github-codeql-extra-queries";
+  return RepositoryPropertyName2;
+})(RepositoryPropertyName || {});
+var KNOWN_REPOSITORY_PROPERTY_NAMES = new Set(
+  Object.values(RepositoryPropertyName)
+);
+
+// src/config/db-config.ts
 var PACK_IDENTIFIER_PATTERN = (function() {
   const alphaNumeric = "[a-z0-9]";
   const alphaNumericDash = "[a-z0-9-]";
diff --git a/lib/analyze-action.js b/lib/analyze-action.js
index 806fd5c46..d20a7e6ff 100644
--- a/lib/analyze-action.js
+++ b/lib/analyze-action.js
@@ -107115,6 +107115,18 @@ function createCacheKeyHash(components) {
 // src/config/db-config.ts
 var jsonschema = __toESM(require_lib2());
 var semver2 = __toESM(require_semver2());
+
+// src/feature-flags/properties.ts
+var RepositoryPropertyName = /* @__PURE__ */ ((RepositoryPropertyName2) => {
+  RepositoryPropertyName2["DISABLE_OVERLAY"] = "github-codeql-disable-overlay";
+  RepositoryPropertyName2["EXTRA_QUERIES"] = "github-codeql-extra-queries";
+  return RepositoryPropertyName2;
+})(RepositoryPropertyName || {});
+var KNOWN_REPOSITORY_PROPERTY_NAMES = new Set(
+  Object.values(RepositoryPropertyName)
+);
+
+// src/config/db-config.ts
 var PACK_IDENTIFIER_PATTERN = (function() {
   const alphaNumeric = "[a-z0-9]";
   const alphaNumericDash = "[a-z0-9-]";
diff --git a/lib/autobuild-action.js b/lib/autobuild-action.js
index 03b8b56cd..6a2dfbad6 100644
--- a/lib/autobuild-action.js
+++ b/lib/autobuild-action.js
@@ -103658,6 +103658,18 @@ var core6 = __toESM(require_core());
 // src/config/db-config.ts
 var jsonschema = __toESM(require_lib2());
 var semver2 = __toESM(require_semver2());
+
+// src/feature-flags/properties.ts
+var RepositoryPropertyName = /* @__PURE__ */ ((RepositoryPropertyName2) => {
+  RepositoryPropertyName2["DISABLE_OVERLAY"] = "github-codeql-disable-overlay";
+  RepositoryPropertyName2["EXTRA_QUERIES"] = "github-codeql-extra-queries";
+  return RepositoryPropertyName2;
+})(RepositoryPropertyName || {});
+var KNOWN_REPOSITORY_PROPERTY_NAMES = new Set(
+  Object.values(RepositoryPropertyName)
+);
+
+// src/config/db-config.ts
 var PACK_IDENTIFIER_PATTERN = (function() {
   const alphaNumeric = "[a-z0-9]";
   const alphaNumericDash = "[a-z0-9-]";
diff --git a/lib/init-action-post.js b/lib/init-action-post.js
index bc1294485..cb91c0bf3 100644
--- a/lib/init-action-post.js
+++ b/lib/init-action-post.js
@@ -164631,6 +164631,18 @@ var RiskAssessment = {
 // src/config/db-config.ts
 var jsonschema = __toESM(require_lib2());
 var semver2 = __toESM(require_semver2());
+
+// src/feature-flags/properties.ts
+var RepositoryPropertyName = /* @__PURE__ */ ((RepositoryPropertyName2) => {
+  RepositoryPropertyName2["DISABLE_OVERLAY"] = "github-codeql-disable-overlay";
+  RepositoryPropertyName2["EXTRA_QUERIES"] = "github-codeql-extra-queries";
+  return RepositoryPropertyName2;
+})(RepositoryPropertyName || {});
+var KNOWN_REPOSITORY_PROPERTY_NAMES = new Set(
+  Object.values(RepositoryPropertyName)
+);
+
+// src/config/db-config.ts
 var PACK_IDENTIFIER_PATTERN = (function() {
   const alphaNumeric = "[a-z0-9]";
   const alphaNumericDash = "[a-z0-9-]";
diff --git a/lib/init-action.js b/lib/init-action.js
index ad82159e7..d78abb1b6 100644
--- a/lib/init-action.js
+++ b/lib/init-action.js
@@ -104283,17 +104283,25 @@ var RepositoryPropertyName = /* @__PURE__ */ ((RepositoryPropertyName2) => {
   RepositoryPropertyName2["EXTRA_QUERIES"] = "github-codeql-extra-queries";
   return RepositoryPropertyName2;
 })(RepositoryPropertyName || {});
+var KNOWN_REPOSITORY_PROPERTY_NAMES = new Set(
+  Object.values(RepositoryPropertyName)
+);
 function isKnownPropertyName(value) {
-  return Object.values(RepositoryPropertyName).includes(
-    value
-  );
+  return KNOWN_REPOSITORY_PROPERTY_NAMES.has(value);
 }
-var mapRepositoryProperties = {
-  ["github-codeql-disable-overlay" /* DISABLE_OVERLAY */]: (value) => value === "true",
-  ["github-codeql-extra-queries" /* EXTRA_QUERIES */]: (value) => value
+var repositoryPropertyParsers = {
+  ["github-codeql-disable-overlay" /* DISABLE_OVERLAY */]: (name, value, logger) => {
+    if (value !== "true" && value !== "false") {
+      logger.warning(
+        `Repository property '${name}' has unexpected value '${value}'. Expected 'true' or 'false'. Defaulting to false.`
+      );
+    }
+    return value === "true";
+  },
+  ["github-codeql-extra-queries" /* EXTRA_QUERIES */]: (_name, value) => value
 };
-function setProperty2(properties, name, value) {
-  properties[name] = mapRepositoryProperties[name](value);
+function setProperty2(properties, name, value, logger) {
+  properties[name] = repositoryPropertyParsers[name](name, value, logger);
 }
 async function loadPropertiesFromApi(gitHubVersion, logger, repositoryNwo) {
   if (gitHubVersion.type === "GitHub Enterprise Server" /* GHES */) {
@@ -104314,11 +104322,16 @@ async function loadPropertiesFromApi(gitHubVersion, logger, repositoryNwo) {
     for (const property of remoteProperties) {
       if (property.property_name === void 0) {
         throw new Error(
-          `Expected property object to have a 'property_name', but got: ${JSON.stringify(property)}`
+          `Expected repository property object to have a 'property_name', but got: ${JSON.stringify(property)}`
+        );
+      }
+      if (typeof property.value !== "string") {
+        throw new Error(
+          `Expected repository property '${property.property_name}' to have a string value, but got: ${JSON.stringify(property)}`
         );
       }
       if (isKnownPropertyName(property.property_name)) {
-        setProperty2(properties, property.property_name, property.value);
+        setProperty2(properties, property.property_name, property.value, logger);
       }
     }
     if (Object.keys(properties).length === 0) {
diff --git a/lib/resolve-environment-action.js b/lib/resolve-environment-action.js
index 8aac361a3..ad7b6c8ec 100644
--- a/lib/resolve-environment-action.js
+++ b/lib/resolve-environment-action.js
@@ -103657,6 +103657,18 @@ var core6 = __toESM(require_core());
 // src/config/db-config.ts
 var jsonschema = __toESM(require_lib2());
 var semver2 = __toESM(require_semver2());
+
+// src/feature-flags/properties.ts
+var RepositoryPropertyName = /* @__PURE__ */ ((RepositoryPropertyName2) => {
+  RepositoryPropertyName2["DISABLE_OVERLAY"] = "github-codeql-disable-overlay";
+  RepositoryPropertyName2["EXTRA_QUERIES"] = "github-codeql-extra-queries";
+  return RepositoryPropertyName2;
+})(RepositoryPropertyName || {});
+var KNOWN_REPOSITORY_PROPERTY_NAMES = new Set(
+  Object.values(RepositoryPropertyName)
+);
+
+// src/config/db-config.ts
 var PACK_IDENTIFIER_PATTERN = (function() {
   const alphaNumeric = "[a-z0-9]";
   const alphaNumericDash = "[a-z0-9-]";
diff --git a/lib/setup-codeql-action.js b/lib/setup-codeql-action.js
index 6a521cc92..099e162ae 100644
--- a/lib/setup-codeql-action.js
+++ b/lib/setup-codeql-action.js
@@ -104651,6 +104651,18 @@ var supportedAnalysisKinds = new Set(Object.values(AnalysisKind));
 // src/config/db-config.ts
 var jsonschema = __toESM(require_lib2());
 var semver5 = __toESM(require_semver2());
+
+// src/feature-flags/properties.ts
+var RepositoryPropertyName = /* @__PURE__ */ ((RepositoryPropertyName2) => {
+  RepositoryPropertyName2["DISABLE_OVERLAY"] = "github-codeql-disable-overlay";
+  RepositoryPropertyName2["EXTRA_QUERIES"] = "github-codeql-extra-queries";
+  return RepositoryPropertyName2;
+})(RepositoryPropertyName || {});
+var KNOWN_REPOSITORY_PROPERTY_NAMES = new Set(
+  Object.values(RepositoryPropertyName)
+);
+
+// src/config/db-config.ts
 var PACK_IDENTIFIER_PATTERN = (function() {
   const alphaNumeric = "[a-z0-9]";
   const alphaNumericDash = "[a-z0-9-]";
diff --git a/lib/start-proxy-action-post.js b/lib/start-proxy-action-post.js
index afed44174..78a4ed2a8 100644
--- a/lib/start-proxy-action-post.js
+++ b/lib/start-proxy-action-post.js
@@ -160888,6 +160888,18 @@ var core6 = __toESM(require_core());
 // src/config/db-config.ts
 var jsonschema = __toESM(require_lib2());
 var semver2 = __toESM(require_semver2());
+
+// src/feature-flags/properties.ts
+var RepositoryPropertyName = /* @__PURE__ */ ((RepositoryPropertyName2) => {
+  RepositoryPropertyName2["DISABLE_OVERLAY"] = "github-codeql-disable-overlay";
+  RepositoryPropertyName2["EXTRA_QUERIES"] = "github-codeql-extra-queries";
+  return RepositoryPropertyName2;
+})(RepositoryPropertyName || {});
+var KNOWN_REPOSITORY_PROPERTY_NAMES = new Set(
+  Object.values(RepositoryPropertyName)
+);
+
+// src/config/db-config.ts
 var PACK_IDENTIFIER_PATTERN = (function() {
   const alphaNumeric = "[a-z0-9]";
   const alphaNumericDash = "[a-z0-9-]";
diff --git a/lib/start-proxy-action.js b/lib/start-proxy-action.js
index 1f83e0a9f..daed18596 100644
--- a/lib/start-proxy-action.js
+++ b/lib/start-proxy-action.js
@@ -121258,6 +121258,18 @@ var supportedAnalysisKinds = new Set(Object.values(AnalysisKind));
 // src/config/db-config.ts
 var jsonschema = __toESM(require_lib2());
 var semver5 = __toESM(require_semver2());
+
+// src/feature-flags/properties.ts
+var RepositoryPropertyName = /* @__PURE__ */ ((RepositoryPropertyName2) => {
+  RepositoryPropertyName2["DISABLE_OVERLAY"] = "github-codeql-disable-overlay";
+  RepositoryPropertyName2["EXTRA_QUERIES"] = "github-codeql-extra-queries";
+  return RepositoryPropertyName2;
+})(RepositoryPropertyName || {});
+var KNOWN_REPOSITORY_PROPERTY_NAMES = new Set(
+  Object.values(RepositoryPropertyName)
+);
+
+// src/config/db-config.ts
 var PACK_IDENTIFIER_PATTERN = (function() {
   const alphaNumeric = "[a-z0-9]";
   const alphaNumericDash = "[a-z0-9-]";
diff --git a/lib/upload-lib.js b/lib/upload-lib.js
index 01383883e..f66b8ce9b 100644
--- a/lib/upload-lib.js
+++ b/lib/upload-lib.js
@@ -106710,6 +106710,18 @@ var core6 = __toESM(require_core());
 // src/config/db-config.ts
 var jsonschema = __toESM(require_lib2());
 var semver2 = __toESM(require_semver2());
+
+// src/feature-flags/properties.ts
+var RepositoryPropertyName = /* @__PURE__ */ ((RepositoryPropertyName2) => {
+  RepositoryPropertyName2["DISABLE_OVERLAY"] = "github-codeql-disable-overlay";
+  RepositoryPropertyName2["EXTRA_QUERIES"] = "github-codeql-extra-queries";
+  return RepositoryPropertyName2;
+})(RepositoryPropertyName || {});
+var KNOWN_REPOSITORY_PROPERTY_NAMES = new Set(
+  Object.values(RepositoryPropertyName)
+);
+
+// src/config/db-config.ts
 var PACK_IDENTIFIER_PATTERN = (function() {
   const alphaNumeric = "[a-z0-9]";
   const alphaNumericDash = "[a-z0-9-]";
diff --git a/lib/upload-sarif-action-post.js b/lib/upload-sarif-action-post.js
index 67c09a211..4e0869c70 100644
--- a/lib/upload-sarif-action-post.js
+++ b/lib/upload-sarif-action-post.js
@@ -161038,6 +161038,18 @@ var core6 = __toESM(require_core());
 // src/config/db-config.ts
 var jsonschema = __toESM(require_lib5());
 var semver2 = __toESM(require_semver2());
+
+// src/feature-flags/properties.ts
+var RepositoryPropertyName = /* @__PURE__ */ ((RepositoryPropertyName2) => {
+  RepositoryPropertyName2["DISABLE_OVERLAY"] = "github-codeql-disable-overlay";
+  RepositoryPropertyName2["EXTRA_QUERIES"] = "github-codeql-extra-queries";
+  return RepositoryPropertyName2;
+})(RepositoryPropertyName || {});
+var KNOWN_REPOSITORY_PROPERTY_NAMES = new Set(
+  Object.values(RepositoryPropertyName)
+);
+
+// src/config/db-config.ts
 var PACK_IDENTIFIER_PATTERN = (function() {
   const alphaNumeric = "[a-z0-9]";
   const alphaNumericDash = "[a-z0-9-]";
diff --git a/lib/upload-sarif-action.js b/lib/upload-sarif-action.js
index 34114e3ea..64189de33 100644
--- a/lib/upload-sarif-action.js
+++ b/lib/upload-sarif-action.js
@@ -107382,6 +107382,18 @@ var path7 = __toESM(require("path"));
 // src/config/db-config.ts
 var jsonschema = __toESM(require_lib2());
 var semver5 = __toESM(require_semver2());
+
+// src/feature-flags/properties.ts
+var RepositoryPropertyName = /* @__PURE__ */ ((RepositoryPropertyName2) => {
+  RepositoryPropertyName2["DISABLE_OVERLAY"] = "github-codeql-disable-overlay";
+  RepositoryPropertyName2["EXTRA_QUERIES"] = "github-codeql-extra-queries";
+  return RepositoryPropertyName2;
+})(RepositoryPropertyName || {});
+var KNOWN_REPOSITORY_PROPERTY_NAMES = new Set(
+  Object.values(RepositoryPropertyName)
+);
+
+// src/config/db-config.ts
 var PACK_IDENTIFIER_PATTERN = (function() {
   const alphaNumeric = "[a-z0-9]";
   const alphaNumericDash = "[a-z0-9-]";
diff --git a/src/feature-flags/properties.test.ts b/src/feature-flags/properties.test.ts
index a7c425002..8cf8ef7cd 100644
--- a/src/feature-flags/properties.test.ts
+++ b/src/feature-flags/properties.test.ts
@@ -28,6 +28,9 @@ test("loadPropertiesFromApi throws if response data is not an array", async (t)
       logger,
       mockRepositoryNwo,
     ),
+    {
+      message: /Expected repository properties API to return an array/,
+    },
   );
 });
 
@@ -48,6 +51,9 @@ test("loadPropertiesFromApi throws if response data contains unexpected objects"
       logger,
       mockRepositoryNwo,
     ),
+    {
+      message: /Expected repository property object to have a 'property_name'/,
+    },
   );
 });
 
@@ -95,3 +101,117 @@ test("loadPropertiesFromApi loads known properties", async (t) => {
   );
   t.deepEqual(response, { "github-codeql-extra-queries": "+queries" });
 });
+
+test("loadPropertiesFromApi parses true boolean property", async (t) => {
+  sinon.stub(api, "getRepositoryProperties").resolves({
+    headers: {},
+    status: 200,
+    url: "",
+    data: [
+      {
+        property_name: "github-codeql-disable-overlay",
+        value: "true",
+      },
+      { property_name: "github-codeql-extra-queries", value: "+queries" },
+    ] satisfies properties.GitHubPropertiesResponse,
+  });
+  const logger = getRunnerLogger(true);
+  const warningSpy = sinon.spy(logger, "warning");
+  const mockRepositoryNwo = parseRepositoryNwo("owner/repo");
+  const response = await properties.loadPropertiesFromApi(
+    {
+      type: util.GitHubVariant.DOTCOM,
+    },
+    logger,
+    mockRepositoryNwo,
+  );
+  t.deepEqual(response, {
+    "github-codeql-disable-overlay": true,
+    "github-codeql-extra-queries": "+queries",
+  });
+  t.true(warningSpy.notCalled);
+});
+
+test("loadPropertiesFromApi parses false boolean property", async (t) => {
+  sinon.stub(api, "getRepositoryProperties").resolves({
+    headers: {},
+    status: 200,
+    url: "",
+    data: [
+      {
+        property_name: "github-codeql-disable-overlay",
+        value: "false",
+      },
+    ] satisfies properties.GitHubPropertiesResponse,
+  });
+  const logger = getRunnerLogger(true);
+  const warningSpy = sinon.spy(logger, "warning");
+  const mockRepositoryNwo = parseRepositoryNwo("owner/repo");
+  const response = await properties.loadPropertiesFromApi(
+    {
+      type: util.GitHubVariant.DOTCOM,
+    },
+    logger,
+    mockRepositoryNwo,
+  );
+  t.deepEqual(response, {
+    "github-codeql-disable-overlay": false,
+  });
+  t.true(warningSpy.notCalled);
+});
+
+test("loadPropertiesFromApi throws if property value is not a string", async (t) => {
+  sinon.stub(api, "getRepositoryProperties").resolves({
+    headers: {},
+    status: 200,
+    url: "",
+    data: [{ property_name: "github-codeql-extra-queries", value: 123 }],
+  });
+  const logger = getRunnerLogger(true);
+  const mockRepositoryNwo = parseRepositoryNwo("owner/repo");
+  await t.throwsAsync(
+    properties.loadPropertiesFromApi(
+      {
+        type: util.GitHubVariant.DOTCOM,
+      },
+      logger,
+      mockRepositoryNwo,
+    ),
+    {
+      message:
+        /Expected repository property 'github-codeql-extra-queries' to have a string value/,
+    },
+  );
+});
+
+test("loadPropertiesFromApi warns if boolean property has unexpected value", async (t) => {
+  sinon.stub(api, "getRepositoryProperties").resolves({
+    headers: {},
+    status: 200,
+    url: "",
+    data: [
+      {
+        property_name: "github-codeql-disable-overlay",
+        value: "yes",
+      },
+    ] satisfies properties.GitHubPropertiesResponse,
+  });
+  const logger = getRunnerLogger(true);
+  const warningSpy = sinon.spy(logger, "warning");
+  const mockRepositoryNwo = parseRepositoryNwo("owner/repo");
+  const response = await properties.loadPropertiesFromApi(
+    {
+      type: util.GitHubVariant.DOTCOM,
+    },
+    logger,
+    mockRepositoryNwo,
+  );
+  t.deepEqual(response, {
+    "github-codeql-disable-overlay": false,
+  });
+  t.true(warningSpy.calledOnce);
+  t.is(
+    warningSpy.firstCall.args[0],
+    "Repository property 'github-codeql-disable-overlay' has unexpected value 'yes'. Expected 'true' or 'false'. Defaulting to false.",
+  );
+});
diff --git a/src/feature-flags/properties.ts b/src/feature-flags/properties.ts
index 70af80129..9477cbad4 100644
--- a/src/feature-flags/properties.ts
+++ b/src/feature-flags/properties.ts
@@ -11,10 +11,12 @@ export enum RepositoryPropertyName {
   EXTRA_QUERIES = "github-codeql-extra-queries",
 }
 
+const KNOWN_REPOSITORY_PROPERTY_NAMES = new Set<string>(
+  Object.values(RepositoryPropertyName),
+);
+
 function isKnownPropertyName(value: string): value is RepositoryPropertyName {
-  return Object.values(RepositoryPropertyName).includes(
-    value as RepositoryPropertyName,
-  );
+  return KNOWN_REPOSITORY_PROPERTY_NAMES.has(value);
 }
 
 type AllRepositoryProperties = {
@@ -24,31 +26,45 @@ type AllRepositoryProperties = {
 
 export type RepositoryProperties = Partial<AllRepositoryProperties>;
 
-const mapRepositoryProperties: {
-  [K in RepositoryPropertyName]: (value: string) => AllRepositoryProperties[K];
+/** Parsers that transform repository properties from the API response into typed values. */
+const repositoryPropertyParsers: {
+  [K in RepositoryPropertyName]: (
+    name: K,
+    value: string,
+    logger: Logger,
+  ) => AllRepositoryProperties[K];
 } = {
-  [RepositoryPropertyName.DISABLE_OVERLAY]: (value) => value === "true",
-  [RepositoryPropertyName.EXTRA_QUERIES]: (value) => value,
+  [RepositoryPropertyName.DISABLE_OVERLAY]: (name, value, logger) => {
+    if (value !== "true" && value !== "false") {
+      logger.warning(
+        `Repository property '${name}' has unexpected value '${value}'. Expected 'true' or 'false'. Defaulting to false.`,
+      );
+    }
+    return value === "true";
+  },
+  [RepositoryPropertyName.EXTRA_QUERIES]: (_name, value) => value,
 };
 
+/** Update the partial set of repository properties with the parsed value of the specified property. */
 function setProperty<K extends RepositoryPropertyName>(
   properties: RepositoryProperties,
   name: K,
   value: string,
+  logger: Logger,
 ): void {
-  properties[name] = mapRepositoryProperties[name](value);
+  properties[name] = repositoryPropertyParsers[name](name, value, logger);
 }
 
 /**
  * A repository property has a name and a value.
  */
-interface GitHubRepositoryProperty {
+export interface GitHubRepositoryProperty {
   property_name: string;
   value: string;
 }
 
 /**
- * The API returns a list of `RepositoryProperty` objects.
+ * The API returns a list of `GitHubRepositoryProperty` objects.
  */
 export type GitHubPropertiesResponse = GitHubRepositoryProperty[];
 
@@ -88,12 +104,18 @@ export async function loadPropertiesFromApi(
     for (const property of remoteProperties) {
       if (property.property_name === undefined) {
         throw new Error(
-          `Expected property object to have a 'property_name', but got: ${JSON.stringify(property)}`,
+          `Expected repository property object to have a 'property_name', but got: ${JSON.stringify(property)}`,
+        );
+      }
+
+      if (typeof property.value !== "string") {
+        throw new Error(
+          `Expected repository property '${property.property_name}' to have a string value, but got: ${JSON.stringify(property)}`,
         );
       }
 
       if (isKnownPropertyName(property.property_name)) {
-        setProperty(properties, property.property_name, property.value);
+        setProperty(properties, property.property_name, property.value, logger);
       }
     }