diff --git a/lib/entry-points.js b/lib/entry-points.js
index ef7547dda..7994d26d9 100644
--- a/lib/entry-points.js
+++ b/lib/entry-points.js
@@ -150444,7 +150444,7 @@ async function initActionState({
   analysisKinds,
   logger,
   enableFileCoverageInformation
-}, userConfig) {
+}, userConfig, repositoryRoot) {
   const languages = await getLanguages(
     codeql,
     languagesInput,
@@ -150480,6 +150480,7 @@ async function initActionState({
   );
   return {
     version: getActionVersion(),
+    repositoryRoot,
     analysisKinds,
     languages,
     buildMode,
@@ -150630,7 +150631,7 @@ async function checkRunnerResources(codeql, features, diskUsage, ramInput, logge
   }
   return new Success(void 0);
 }
-async function checkOverlayEnablement(codeql, features, languages, sourceRoot, buildMode, ramInput, codeScanningConfig, repositoryProperties, gitVersion, logger) {
+async function checkOverlayEnablement(codeql, features, languages, repositoryRoot, sourceRoot, buildMode, ramInput, codeScanningConfig, repositoryProperties, gitVersion, logger) {
   const modeEnv = process.env.CODEQL_OVERLAY_DATABASE_MODE;
   if (modeEnv === "overlay" /* Overlay */ || modeEnv === "overlay-base" /* OverlayBase */ || modeEnv === "none" /* None */) {
     logger.info(
@@ -150645,6 +150646,7 @@ async function checkOverlayEnablement(codeql, features, languages, sourceRoot, b
       true,
       codeql,
       languages,
+      repositoryRoot,
       sourceRoot,
       buildMode,
       gitVersion,
@@ -150717,13 +150719,14 @@ async function checkOverlayEnablement(codeql, features, languages, sourceRoot, b
     false,
     codeql,
     languages,
+    repositoryRoot,
     sourceRoot,
     buildMode,
     gitVersion,
     logger
   );
 }
-async function validateOverlayDatabaseMode(overlayDatabaseMode, useOverlayDatabaseCaching, overlayModeSetExplicitly, codeql, languages, sourceRoot, buildMode, gitVersion, logger) {
+async function validateOverlayDatabaseMode(overlayDatabaseMode, useOverlayDatabaseCaching, overlayModeSetExplicitly, codeql, languages, repositoryRoot, sourceRoot, buildMode, gitVersion, logger) {
   if (buildMode !== "none" /* None */ && (await Promise.all(
     languages.map(
       async (l) => l !== "go" /* go */ && // Workaround to allow overlay analysis for Go with any build
@@ -150744,14 +150747,13 @@ async function validateOverlayDatabaseMode(overlayDatabaseMode, useOverlayDataba
     );
     return new Failure("incompatible-codeql" /* IncompatibleCodeQl */);
   }
-  const gitRoot = await getGitRoot(sourceRoot);
-  if (gitRoot === void 0) {
+  if (repositoryRoot === void 0) {
     logger.warning(
       `Cannot build an ${overlayDatabaseMode} database because the source root "${sourceRoot}" is not inside a git repository. Falling back to creating a normal full database instead.`
     );
     return new Failure("no-git-root" /* NoGitRoot */);
   }
-  if (hasSubmodules(gitRoot)) {
+  if (hasSubmodules(repositoryRoot)) {
     if (gitVersion === void 0) {
       logger.warning(
         `Cannot build an ${overlayDatabaseMode} database because the repository has submodules and the Git version could not be determined. Falling back to creating a normal full database instead.`
@@ -150886,8 +150888,9 @@ async function determineUserConfig(action, tempDir, inputs) {
 async function initConfig(actionState, inputs) {
   const { logger, features } = actionState;
   const { tempDir } = inputs;
+  const repositoryRoot = await getGitRoot(inputs.sourceRoot);
   const userConfig = await determineUserConfig(actionState, tempDir, inputs);
-  const config = await initActionState(inputs, userConfig);
+  const config = await initActionState(inputs, userConfig, repositoryRoot);
   if (config.analysisKinds.length === 1 && isCodeQualityEnabled(config)) {
     if (hasQueryCustomisation(config.computedConfig)) {
       throw new ConfigurationError(
@@ -150940,6 +150943,7 @@ async function initConfig(actionState, inputs) {
     inputs.codeql,
     inputs.features,
     config.languages,
+    repositoryRoot,
     inputs.sourceRoot,
     config.buildMode,
     inputs.ramInput,
@@ -153801,8 +153805,27 @@ var CodeQLAnalysisError = class extends Error {
   message;
   error;
 };
-function determineCheckoutPath(action) {
-  return action.actions.getRequiredInput("checkout_path");
+async function determineCheckoutPath(action) {
+  const checkoutPathInput = action.actions.getRequiredInput("checkout_path");
+  const repositoryRoot = await getGitRoot(checkoutPathInput);
+  if (repositoryRoot === void 0) {
+    action.logger.warning(
+      [
+        `The directory at '${checkoutPathInput}' is not in the work tree of a git repository.`,
+        "If the repository being analyzed is checked out elsewhere,",
+        "you must explicitly set the 'checkout_path' input for the 'codeql-action/analyze' step to",
+        "the checkout path."
+      ].join(" ")
+    );
+  } else if (repositoryRoot !== path16.resolve(checkoutPathInput)) {
+    action.logger.warning(
+      [
+        `The directory at '${checkoutPathInput}' is not the root of the repository ('${repositoryRoot}').`,
+        "Set the 'checkout_path' input for the 'codeql-action/analyze' step to the root path of the checkout."
+      ].join(" ")
+    );
+  }
+  return checkoutPathInput;
 }
 async function setupPythonExtractor(logger) {
   const codeqlPython = process.env["CODEQL_PYTHON"];
@@ -156615,7 +156638,7 @@ async function run(action) {
       getOptionalInput("ram") || process.env["CODEQL_RAM"],
       logger
     );
-    const checkoutPath = determineCheckoutPath(action);
+    const checkoutPath = await determineCheckoutPath(action);
     const diffRangePackDir = await setupDiffInformedQueryRun(
       logger,
       checkoutPath
diff --git a/src/analyze-action.test.ts b/src/analyze-action.test.ts
index 923908a64..ffba5a03d 100644
--- a/src/analyze-action.test.ts
+++ b/src/analyze-action.test.ts
@@ -45,6 +45,7 @@ test.serial(
       requiredInputStub.withArgs("token").returns("fake-token");
       requiredInputStub.withArgs("upload-database").returns("false");
       requiredInputStub.withArgs("output").returns("out");
+      requiredInputStub.withArgs("checkout_path").returns("");
       const optionalInputStub = sinon.stub(actionsUtil, "getOptionalInput");
       optionalInputStub.withArgs("expect-error").returns("false");
       sinon.stub(api, "getGitHubVersion").resolves(gitHubVersion);
@@ -104,6 +105,7 @@ test.serial(
       requiredInputStub.withArgs("token").returns("fake-token");
       requiredInputStub.withArgs("upload-database").returns("false");
       requiredInputStub.withArgs("output").returns("out");
+      requiredInputStub.withArgs("checkout_path").returns("");
       const optionalInputStub = sinon.stub(actionsUtil, "getOptionalInput");
       optionalInputStub.withArgs("expect-error").returns("false");
       sinon.stub(api, "getGitHubVersion").resolves(gitHubVersion);
diff --git a/src/analyze-action.ts b/src/analyze-action.ts
index 67b025ead..7c117f75a 100644
--- a/src/analyze-action.ts
+++ b/src/analyze-action.ts
@@ -310,7 +310,7 @@ async function run(action: ActionState<["Base", "Logger", "Env", "Actions"]>) {
       logger,
     );
 
-    const checkoutPath = determineCheckoutPath(action);
+    const checkoutPath = await determineCheckoutPath(action);
 
     // Setup diff informed analysis if needed (based on whether init created the file)
     const diffRangePackDir = await setupDiffInformedQueryRun(
diff --git a/src/analyze.ts b/src/analyze.ts
index 3580f80aa..306ccd434 100644
--- a/src/analyze.ts
+++ b/src/analyze.ts
@@ -22,6 +22,7 @@ import {
 } from "./diff-informed-analysis-utils";
 import { EnvVar } from "./environment";
 import { FeatureEnablement, Feature } from "./feature-flags";
+import { getGitRoot } from "./git-utils";
 import { BuiltInLanguage, Language } from "./languages";
 import { Logger, withGroupAsync } from "./logging";
 import { OverlayDatabaseMode } from "./overlay/overlay-database-mode";
@@ -93,8 +94,33 @@ export interface QueriesStatusReport
  *
  * @param action The action state.
  */
-export function determineCheckoutPath(action: ActionState<["Actions"]>) {
-  return action.actions.getRequiredInput("checkout_path");
+export async function determineCheckoutPath(
+  action: ActionState<["Logger", "Actions"]>,
+) {
+  const checkoutPathInput = action.actions.getRequiredInput("checkout_path");
+
+  // Try to obtain the root path of the repository and validate that it matches the input.
+  const repositoryRoot = await getGitRoot(checkoutPathInput);
+
+  if (repositoryRoot === undefined) {
+    action.logger.warning(
+      [
+        `The directory at '${checkoutPathInput}' is not in the work tree of a git repository.`,
+        "If the repository being analyzed is checked out elsewhere,",
+        "you must explicitly set the 'checkout_path' input for the 'codeql-action/analyze' step to",
+        "the checkout path.",
+      ].join(" "),
+    );
+  } else if (repositoryRoot !== path.resolve(checkoutPathInput)) {
+    action.logger.warning(
+      [
+        `The directory at '${checkoutPathInput}' is not the root of the repository ('${repositoryRoot}').`,
+        "Set the 'checkout_path' input for the 'codeql-action/analyze' step to the root path of the checkout.",
+      ].join(" "),
+    );
+  }
+
+  return checkoutPathInput;
 }
 
 async function setupPythonExtractor(logger: Logger) {
diff --git a/src/config-utils.test.ts b/src/config-utils.test.ts
index 29d72f3af..ec18bec45 100644
--- a/src/config-utils.test.ts
+++ b/src/config-utils.test.ts
@@ -172,6 +172,7 @@ test.serial("load empty config", async (t) => {
       createTestInitConfigInputs({
         languagesInput: languages,
         repository: { owner: "github", repo: "example" },
+        sourceRoot: tempDir,
         tempDir,
         codeql,
         logger,
@@ -186,6 +187,7 @@ test.serial("load empty config", async (t) => {
         logger,
       }),
       {},
+      undefined,
     );
 
     t.deepEqual(config, expectedConfig);
@@ -216,6 +218,7 @@ test.serial("load code quality config", async (t) => {
         analysisKinds: [AnalysisKind.CodeQuality],
         languagesInput: languages,
         repository: { owner: "github", repo: "example" },
+        sourceRoot: tempDir,
         tempDir,
         codeql,
         logger,
@@ -296,6 +299,7 @@ test.serial(
             analysisKinds: [AnalysisKind.CodeQuality],
             languagesInput: languages,
             repository: { owner: "github", repo: "example" },
+            sourceRoot: tempDir,
             tempDir,
             codeql,
             repositoryProperties,
@@ -512,6 +516,7 @@ test.serial("load non-empty input", async (t) => {
     // And the config we expect it to parse to
     const expectedConfig = createTestConfig({
       languages: [BuiltInLanguage.javascript],
+      repositoryRoot: undefined,
       buildMode: BuildMode.None,
       originalUserInput: userConfig,
       computedConfig: userConfig,
@@ -532,6 +537,7 @@ test.serial("load non-empty input", async (t) => {
       state,
       createTestInitConfigInputs({
         languagesInput,
+        sourceRoot: tempDir,
         buildModeInput: "none",
         configFile: configFilePath,
         debugArtifactName: "my-artifact",
@@ -1092,11 +1098,6 @@ const checkOverlayEnablementMacro = makeMacro({
             return lang === BuiltInLanguage.java;
           });
 
-        // Mock git root detection
-        if (setup.gitRoot !== undefined) {
-          sinon.stub(gitUtils, "getGitRoot").resolves(setup.gitRoot);
-        }
-
         // Mock submodule detection
         sinon.stub(gitUtils, "hasSubmodules").returns(setup.hasSubmodules);
 
@@ -1109,6 +1110,7 @@ const checkOverlayEnablementMacro = makeMacro({
           codeql,
           features,
           setup.languages,
+          setup.gitRoot, // repositoryRoot
           tempDir, // sourceRoot
           setup.buildMode,
           undefined,
diff --git a/src/config-utils.ts b/src/config-utils.ts
index 288b4f02f..37337b68d 100644
--- a/src/config-utils.ts
+++ b/src/config-utils.ts
@@ -385,6 +385,7 @@ export async function initActionState(
     enableFileCoverageInformation,
   }: InitConfigInputs,
   userConfig: UserConfig,
+  repositoryRoot: string | undefined,
 ): Promise<Config> {
   const languages = await getLanguages(
     codeql,
@@ -436,6 +437,7 @@ export async function initActionState(
 
   return {
     version: getActionVersion(),
+    repositoryRoot,
     analysisKinds,
     languages,
     buildMode,
@@ -718,6 +720,7 @@ export async function checkOverlayEnablement(
   codeql: CodeQL,
   features: FeatureEnablement,
   languages: Language[],
+  repositoryRoot: string | undefined,
   sourceRoot: string,
   buildMode: BuildMode | undefined,
   ramInput: string | undefined,
@@ -747,6 +750,7 @@ export async function checkOverlayEnablement(
       true,
       codeql,
       languages,
+      repositoryRoot,
       sourceRoot,
       buildMode,
       gitVersion,
@@ -836,6 +840,7 @@ export async function checkOverlayEnablement(
     false,
     codeql,
     languages,
+    repositoryRoot,
     sourceRoot,
     buildMode,
     gitVersion,
@@ -855,6 +860,7 @@ async function validateOverlayDatabaseMode(
   overlayModeSetExplicitly: boolean,
   codeql: CodeQL,
   languages: Language[],
+  repositoryRoot: string | undefined,
   sourceRoot: string,
   buildMode: BuildMode | undefined,
   gitVersion: GitVersionInfo | undefined,
@@ -890,8 +896,7 @@ async function validateOverlayDatabaseMode(
     );
     return new Failure(OverlayDisabledReason.IncompatibleCodeQl);
   }
-  const gitRoot = await getGitRoot(sourceRoot);
-  if (gitRoot === undefined) {
+  if (repositoryRoot === undefined) {
     logger.warning(
       `Cannot build an ${overlayDatabaseMode} database because ` +
         `the source root "${sourceRoot}" is not inside a git repository. ` +
@@ -899,7 +904,7 @@ async function validateOverlayDatabaseMode(
     );
     return new Failure(OverlayDisabledReason.NoGitRoot);
   }
-  if (hasSubmodules(gitRoot)) {
+  if (hasSubmodules(repositoryRoot)) {
     if (gitVersion === undefined) {
       logger.warning(
         `Cannot build an ${overlayDatabaseMode} database because ` +
@@ -1160,9 +1165,11 @@ export async function initConfig(
   const { logger, features } = actionState;
   const { tempDir } = inputs;
 
+  const repositoryRoot = await getGitRoot(inputs.sourceRoot);
+
   const userConfig = await determineUserConfig(actionState, tempDir, inputs);
 
-  const config = await initActionState(inputs, userConfig);
+  const config = await initActionState(inputs, userConfig, repositoryRoot);
 
   // If Code Quality analysis is the only enabled analysis kind, then we will initialise
   // the database for Code Quality. That entails disabling the default queries and only
@@ -1244,6 +1251,7 @@ export async function initConfig(
     inputs.codeql,
     inputs.features,
     config.languages,
+    repositoryRoot,
     inputs.sourceRoot,
     config.buildMode,
     inputs.ramInput,
diff --git a/src/config/action-config.ts b/src/config/action-config.ts
index de6882e77..2b69141d2 100644
--- a/src/config/action-config.ts
+++ b/src/config/action-config.ts
@@ -16,6 +16,11 @@ export interface Config {
    * The version of the CodeQL Action that the configuration is for.
    */
   version: string;
+  /**
+   * The path at which the repository being analysed is checked out at, if available.
+   * Persisted in the CodeQL Action configuration state, so that we can consult it in later workflow steps.
+   */
+  repositoryRoot: string | undefined;
   /**
    * Set of analysis kinds that are enabled.
    */
diff --git a/src/testing-utils.ts b/src/testing-utils.ts
index f15cee2e7..b50d51c94 100644
--- a/src/testing-utils.ts
+++ b/src/testing-utils.ts
@@ -968,6 +968,7 @@ export function createTestConfig(overrides: Partial<Config>): Config {
     {},
     {
       version: getActionVersion(),
+      repositoryRoot: undefined,
       analysisKinds: [AnalysisKind.CodeScanning],
       languages: [],
       buildMode: undefined,