diff --git a/lib/entry-points.js b/lib/entry-points.js
index 7994d26d9..ca6dd881b 100644
--- a/lib/entry-points.js
+++ b/lib/entry-points.js
@@ -153805,7 +153805,7 @@ var CodeQLAnalysisError = class extends Error {
   message;
   error;
 };
-async function determineCheckoutPath(action) {
+async function determineCheckoutPath(action, config) {
   const checkoutPathInput = action.actions.getRequiredInput("checkout_path");
   const repositoryRoot = await getGitRoot(checkoutPathInput);
   if (repositoryRoot === void 0) {
@@ -153824,6 +153824,15 @@ async function determineCheckoutPath(action) {
         "Set the 'checkout_path' input for the 'codeql-action/analyze' step to the root path of the checkout."
       ].join(" ")
     );
+  } else if (config.repositoryRoot !== void 0 && repositoryRoot !== config.repositoryRoot) {
+    action.logger.warning(
+      [
+        `The repository path at '${repositoryRoot}' does not match that found by the 'codeql-action/init' step: '${config.repositoryRoot}'.`,
+        "Ensure that the 'checkout_path' input for the 'codeql-action/analyze' step is set to the path of the same repository that",
+        "the 'codeql-action/init' step determined. This is either the GitHub Actions workspace or the repository root corresponding to",
+        "the 'source-root' input if that was provided."
+      ].join(" ")
+    );
   }
   return checkoutPathInput;
 }
@@ -156638,7 +156647,7 @@ async function run(action) {
       getOptionalInput("ram") || process.env["CODEQL_RAM"],
       logger
     );
-    const checkoutPath = await determineCheckoutPath(action);
+    const checkoutPath = await determineCheckoutPath(action, config);
     const diffRangePackDir = await setupDiffInformedQueryRun(
       logger,
       checkoutPath
diff --git a/src/analyze-action.ts b/src/analyze-action.ts
index 7c117f75a..8cc13c1ba 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 = await determineCheckoutPath(action);
+    const checkoutPath = await determineCheckoutPath(action, config);
 
     // 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 306ccd434..f1a1841f3 100644
--- a/src/analyze.ts
+++ b/src/analyze.ts
@@ -93,9 +93,11 @@ export interface QueriesStatusReport
  * refers to the root of a repository.
  *
  * @param action The action state.
+ * @param config The CodeQL Action configuration state.
  */
 export async function determineCheckoutPath(
   action: ActionState<["Logger", "Actions"]>,
+  config: configUtils.Config,
 ) {
   const checkoutPathInput = action.actions.getRequiredInput("checkout_path");
 
@@ -118,6 +120,19 @@ export async function determineCheckoutPath(
         "Set the 'checkout_path' input for the 'codeql-action/analyze' step to the root path of the checkout.",
       ].join(" "),
     );
+  } else if (
+    config.repositoryRoot !== undefined &&
+    repositoryRoot !== config.repositoryRoot
+  ) {
+    // The repository root that was persisted by the `init` step doesn't match the one we have found here.
+    action.logger.warning(
+      [
+        `The repository path at '${repositoryRoot}' does not match that found by the 'codeql-action/init' step: '${config.repositoryRoot}'.`,
+        "Ensure that the 'checkout_path' input for the 'codeql-action/analyze' step is set to the path of the same repository that",
+        "the 'codeql-action/init' step determined. This is either the GitHub Actions workspace or the repository root corresponding to",
+        "the 'source-root' input if that was provided.",
+      ].join(" "),
+    );
   }
 
   return checkoutPathInput;