diff --git a/src/init-action.ts b/src/init-action.ts
index 533f8eaef..11e851491 100644
--- a/src/init-action.ts
+++ b/src/init-action.ts
@@ -785,7 +785,9 @@ async function run() {
       );
       config.augmentationProperties.overlayDatabaseMode =
         OverlayDatabaseMode.None;
-      cleanupDatabaseClusterDirectory(config, logger);
+      cleanupDatabaseClusterDirectory(config, logger, {
+        disableExistingDirectoryWarning: true,
+      });
       await runDatabaseInitCluster(
         databaseInitEnvironment,
         codeql,
diff --git a/src/init.test.ts b/src/init.test.ts
index 03f456d11..740435f6a 100644
--- a/src/init.test.ts
+++ b/src/init.test.ts
@@ -92,6 +92,7 @@ for (const { runnerEnv, ErrorConstructor, message } of [
           cleanupDatabaseClusterDirectory(
             createTestConfig({ dbLocation }),
             getRecordingLogger(messages),
+            {},
             () => {
               throw new Error(rmSyncError);
             },
@@ -112,6 +113,33 @@ for (const { runnerEnv, ErrorConstructor, message } of [
   });
 }
 
+test("cleanupDatabaseClusterDirectory can disable warning with options", async (t) => {
+  await withTmpDir(async (tmpDir: string) => {
+    const dbLocation = path.resolve(tmpDir, "dbs");
+    fs.mkdirSync(dbLocation, { recursive: true });
+
+    const fileToCleanUp = path.resolve(dbLocation, "something-to-cleanup.txt");
+    fs.writeFileSync(fileToCleanUp, "");
+
+    const messages: LoggedMessage[] = [];
+    cleanupDatabaseClusterDirectory(
+      createTestConfig({ dbLocation }),
+      getRecordingLogger(messages),
+      { disableExistingDirectoryWarning: true },
+    );
+
+    // Should only have the info message, not the warning
+    t.is(messages.length, 1);
+    t.is(messages[0].type, "info");
+    t.is(
+      messages[0].message,
+      `Cleaned up database cluster directory ${dbLocation}.`,
+    );
+
+    t.false(fs.existsSync(fileToCleanUp));
+  });
+});
+
 type PackInfo = {
   language: KnownLanguage;
   packinfoContents: string | undefined;
diff --git a/src/init.ts b/src/init.ts
index 3e6f6b650..a62929b92 100644
--- a/src/init.ts
+++ b/src/init.ts
@@ -238,6 +238,7 @@ export async function checkInstallPython311(
 export function cleanupDatabaseClusterDirectory(
   config: configUtils.Config,
   logger: Logger,
+  options: { disableExistingDirectoryWarning?: boolean } = {},
   // We can't stub the fs module in tests, so we allow the caller to override the rmSync function
   // for testing.
   rmSync = fs.rmSync,
@@ -247,9 +248,11 @@ export function cleanupDatabaseClusterDirectory(
     (fs.statSync(config.dbLocation).isFile() ||
       fs.readdirSync(config.dbLocation).length > 0)
   ) {
-    logger.warning(
-      `The database cluster directory ${config.dbLocation} must be empty. Attempting to clean it up.`,
-    );
+    if (!options.disableExistingDirectoryWarning) {
+      logger.warning(
+        `The database cluster directory ${config.dbLocation} must be empty. Attempting to clean it up.`,
+      );
+    }
     try {
       rmSync(config.dbLocation, {
         force: true,