diff --git a/lib/init-action.js b/lib/init-action.js
index 6b9af9b69..34b9335f5 100644
--- a/lib/init-action.js
+++ b/lib/init-action.js
@@ -109094,15 +109094,19 @@ function cleanupDatabaseClusterDirectory(config, logger, options = {}, rmSync2 =
   }
 }
 async function getFileCoverageInformationEnabled(debugMode, codeql, features, repositoryProperties) {
-  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() || // Allow repositories to opt in to file coverage information on PRs
-    // using a repository property.
-    repositoryProperties["github-codeql-file-coverage-on-prs" /* FILE_COVERAGE_ON_PRS */] === true || !await features.getValue("skip_file_coverage_on_prs" /* SkipFileCoverageOnPrs */, codeql)
-  );
+  if (debugMode) {
+    return { enabled: true, enabledByRepositoryProperty: false };
+  }
+  if (!isAnalyzingPullRequest()) {
+    return { enabled: true, enabledByRepositoryProperty: false };
+  }
+  if (!await features.getValue("skip_file_coverage_on_prs" /* SkipFileCoverageOnPrs */, codeql)) {
+    return { enabled: true, enabledByRepositoryProperty: false };
+  }
+  if (repositoryProperties["github-codeql-file-coverage-on-prs" /* FILE_COVERAGE_ON_PRS */] === true) {
+    return { enabled: true, enabledByRepositoryProperty: true };
+  }
+  return { enabled: false, enabledByRepositoryProperty: false };
 }
 
 // src/status-report.ts
@@ -109714,6 +109718,12 @@ async function run(startedAt) {
     analysisKinds = await getAnalysisKinds(logger);
     const debugMode = getOptionalInput("debug") === "true" || core13.isDebug();
     const repositoryProperties = repositoryPropertiesResult.orElse({});
+    const fileCoverageResult = await getFileCoverageInformationEnabled(
+      debugMode,
+      codeql,
+      features,
+      repositoryProperties
+    );
     config = await initConfig2(features, {
       analysisKinds,
       languagesInput: getOptionalInput("languages"),
@@ -109742,12 +109752,7 @@ async function run(startedAt) {
       apiDetails,
       features,
       repositoryProperties,
-      enableFileCoverageInformation: await getFileCoverageInformationEnabled(
-        debugMode,
-        codeql,
-        features,
-        repositoryProperties
-      ),
+      enableFileCoverageInformation: fileCoverageResult.enabled,
       logger
     });
     if (repositoryPropertiesResult.isFailure()) {
@@ -109762,7 +109767,7 @@ async function run(startedAt) {
         )
       );
     }
-    if (config.enableFileCoverageInformation && isAnalyzingPullRequest() && await features.getValue("skip_file_coverage_on_prs" /* SkipFileCoverageOnPrs */, codeql) && repositoryProperties["github-codeql-file-coverage-on-prs" /* FILE_COVERAGE_ON_PRS */] === true) {
+    if (fileCoverageResult.enabledByRepositoryProperty) {
       addNoLanguageDiagnostic(
         config,
         makeTelemetryDiagnostic(
diff --git a/src/init-action.ts b/src/init-action.ts
index 6a386ed7a..577292ecd 100644
--- a/src/init-action.ts
+++ b/src/init-action.ts
@@ -14,7 +14,6 @@ import {
   getOptionalInput,
   getRequiredInput,
   getTemporaryDirectory,
-  isAnalyzingPullRequest,
   persistInputs,
 } from "./actions-util";
 import { AnalysisKind, getAnalysisKinds } from "./analyses";
@@ -43,7 +42,6 @@ import { Feature, FeatureEnablement, initFeatures } from "./feature-flags";
 import {
   loadPropertiesFromApi,
   RepositoryProperties,
-  RepositoryPropertyName,
 } from "./feature-flags/properties";
 import {
   checkInstallPython311,
@@ -349,6 +347,13 @@ async function run(startedAt: Date) {
     analysisKinds = await getAnalysisKinds(logger);
     const debugMode = getOptionalInput("debug") === "true" || core.isDebug();
     const repositoryProperties = repositoryPropertiesResult.orElse({});
+    const fileCoverageResult = await getFileCoverageInformationEnabled(
+      debugMode,
+      codeql,
+      features,
+      repositoryProperties,
+    );
+
     config = await initConfig(features, {
       analysisKinds,
       languagesInput: getOptionalInput("languages"),
@@ -379,12 +384,7 @@ async function run(startedAt: Date) {
       apiDetails,
       features,
       repositoryProperties,
-      enableFileCoverageInformation: await getFileCoverageInformationEnabled(
-        debugMode,
-        codeql,
-        features,
-        repositoryProperties,
-      ),
+      enableFileCoverageInformation: fileCoverageResult.enabled,
       logger,
     });
 
@@ -401,12 +401,7 @@ async function run(startedAt: Date) {
       );
     }
 
-    if (
-      config.enableFileCoverageInformation &&
-      isAnalyzingPullRequest() &&
-      (await features.getValue(Feature.SkipFileCoverageOnPrs, codeql)) &&
-      repositoryProperties[RepositoryPropertyName.FILE_COVERAGE_ON_PRS] === true
-    ) {
+    if (fileCoverageResult.enabledByRepositoryProperty) {
       addNoLanguageDiagnostic(
         config,
         makeTelemetryDiagnostic(
diff --git a/src/init.test.ts b/src/init.test.ts
index dbc4b4c30..c37d1c1e6 100644
--- a/src/init.test.ts
+++ b/src/init.test.ts
@@ -452,14 +452,14 @@ test(
 );
 
 test("file coverage information enabled when debugMode is true", async (t) => {
-  t.true(
-    await getFileCoverageInformationEnabled(
-      true, // debugMode
-      createStubCodeQL({}),
-      createFeatures([Feature.SkipFileCoverageOnPrs]),
-      {},
-    ),
+  const result = await getFileCoverageInformationEnabled(
+    true, // debugMode
+    createStubCodeQL({}),
+    createFeatures([Feature.SkipFileCoverageOnPrs]),
+    {},
   );
+  t.true(result.enabled);
+  t.false(result.enabledByRepositoryProperty);
 });
 
 test.serial(
@@ -467,14 +467,14 @@ test.serial(
   async (t) => {
     sinon.stub(actionsUtil, "isAnalyzingPullRequest").returns(false);
 
-    t.true(
-      await getFileCoverageInformationEnabled(
-        false, // debugMode
-        createStubCodeQL({}),
-        createFeatures([Feature.SkipFileCoverageOnPrs]),
-        {},
-      ),
+    const result = await getFileCoverageInformationEnabled(
+      false, // debugMode
+      createStubCodeQL({}),
+      createFeatures([Feature.SkipFileCoverageOnPrs]),
+      {},
     );
+    t.true(result.enabled);
+    t.false(result.enabledByRepositoryProperty);
   },
 );
 
@@ -483,14 +483,14 @@ test.serial(
   async (t) => {
     sinon.stub(actionsUtil, "isAnalyzingPullRequest").returns(true);
 
-    t.true(
-      await getFileCoverageInformationEnabled(
-        false, // debugMode
-        createStubCodeQL({}),
-        createFeatures([]),
-        {},
-      ),
+    const result = await getFileCoverageInformationEnabled(
+      false, // debugMode
+      createStubCodeQL({}),
+      createFeatures([]),
+      {},
     );
+    t.true(result.enabled);
+    t.false(result.enabledByRepositoryProperty);
   },
 );
 
@@ -499,16 +499,16 @@ test.serial(
   async (t) => {
     sinon.stub(actionsUtil, "isAnalyzingPullRequest").returns(true);
 
-    t.true(
-      await getFileCoverageInformationEnabled(
-        false, // debugMode
-        createStubCodeQL({}),
-        createFeatures([Feature.SkipFileCoverageOnPrs]),
-        {
-          "github-codeql-file-coverage-on-prs": true,
-        },
-      ),
+    const result = await getFileCoverageInformationEnabled(
+      false, // debugMode
+      createStubCodeQL({}),
+      createFeatures([Feature.SkipFileCoverageOnPrs]),
+      {
+        "github-codeql-file-coverage-on-prs": true,
+      },
     );
+    t.true(result.enabled);
+    t.true(result.enabledByRepositoryProperty);
   },
 );
 
@@ -517,13 +517,13 @@ test.serial(
   async (t) => {
     sinon.stub(actionsUtil, "isAnalyzingPullRequest").returns(true);
 
-    t.false(
-      await getFileCoverageInformationEnabled(
-        false, // debugMode
-        createStubCodeQL({}),
-        createFeatures([Feature.SkipFileCoverageOnPrs]),
-        {},
-      ),
+    const result = await getFileCoverageInformationEnabled(
+      false, // debugMode
+      createStubCodeQL({}),
+      createFeatures([Feature.SkipFileCoverageOnPrs]),
+      {},
     );
+    t.false(result.enabled);
+    t.false(result.enabledByRepositoryProperty);
   },
 );
diff --git a/src/init.ts b/src/init.ts
index b5e90b68b..a1c6b2108 100644
--- a/src/init.ts
+++ b/src/init.ts
@@ -306,18 +306,32 @@ export async function getFileCoverageInformationEnabled(
   codeql: CodeQL,
   features: FeatureEnablement,
   repositoryProperties: RepositoryProperties,
-): 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() ||
-    // Allow repositories to opt in to file coverage information on PRs
-    // using a repository property.
-    repositoryProperties[RepositoryPropertyName.FILE_COVERAGE_ON_PRS] ===
-      true ||
-    !(await features.getValue(Feature.SkipFileCoverageOnPrs, codeql))
-  );
+): Promise<{
+  enabled: boolean;
+  enabledByRepositoryProperty: boolean;
+}> {
+  // Always enable file coverage information in debug mode
+  if (debugMode) {
+    return { enabled: true, enabledByRepositoryProperty: false };
+  }
+  // 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.
+  if (!isAnalyzingPullRequest()) {
+    return { enabled: true, enabledByRepositoryProperty: false };
+  }
+  // If the feature is disabled, then maintain the previous behavior of
+  // unconditionally computing file coverage information.
+  if (!(await features.getValue(Feature.SkipFileCoverageOnPrs, codeql))) {
+    return { enabled: true, enabledByRepositoryProperty: false };
+  }
+  // Allow repositories to opt in to file coverage information on PRs
+  // using a repository property.
+  if (
+    repositoryProperties[RepositoryPropertyName.FILE_COVERAGE_ON_PRS] === true
+  ) {
+    return { enabled: true, enabledByRepositoryProperty: true };
+  }
+  // Otherwise, disable file coverage information on PRs to speed up analysis.
+  return { enabled: false, enabledByRepositoryProperty: false };
 }