diff --git a/dist/index.js b/dist/index.js
index 0a33ea1..e83c1b0 100644
--- a/dist/index.js
+++ b/dist/index.js
@@ -7683,6 +7683,12 @@ class GitCommandManager {
             yield this.execGit(args);
         });
     }
+    submoduleStatus() {
+        return __awaiter(this, void 0, void 0, function* () {
+            const output = yield this.execGit(['submodule', 'status'], true);
+            return output.exitCode === 0;
+        });
+    }
     tagExists(pattern) {
         return __awaiter(this, void 0, void 0, function* () {
             const output = yield this.execGit(['tag', '--list', pattern]);
@@ -9436,6 +9442,10 @@ function prepareExistingDirectory(git, repositoryPath, repositoryUrl, clean, ref
                     }
                 }
                 core.endGroup();
+                // Check for submodules and delete any existing files if submodules are present
+                if (!(yield git.submoduleStatus())) {
+                    remove = true;
+                }
                 // Clean
                 if (clean) {
                     core.startGroup('Cleaning the repository');
diff --git a/src/git-command-manager.ts b/src/git-command-manager.ts
index 01aedfe..731fbb2 100644
--- a/src/git-command-manager.ts
+++ b/src/git-command-manager.ts
@@ -41,6 +41,7 @@ export interface IGitCommandManager {
   submoduleForeach(command: string, recursive: boolean): Promise<string>
   submoduleSync(recursive: boolean): Promise<void>
   submoduleUpdate(fetchDepth: number, recursive: boolean): Promise<void>
+  submoduleStatus(): Promise<boolean>
   tagExists(pattern: string): Promise<boolean>
   tryClean(): Promise<boolean>
   tryConfigUnset(configKey: string, globalConfig?: boolean): Promise<boolean>
@@ -357,6 +358,11 @@ class GitCommandManager {
     await this.execGit(args)
   }
 
+  async submoduleStatus(): Promise<boolean> {
+    const output = await this.execGit(['submodule', 'status'], true)
+    return output.exitCode === 0
+  }
+
   async tagExists(pattern: string): Promise<boolean> {
     const output = await this.execGit(['tag', '--list', pattern])
     return !!output.stdout.trim()
diff --git a/src/git-directory-helper.ts b/src/git-directory-helper.ts
index 2979e97..ac61454 100644
--- a/src/git-directory-helper.ts
+++ b/src/git-directory-helper.ts
@@ -81,6 +81,11 @@ export async function prepareExistingDirectory(
       }
       core.endGroup()
 
+      // Check for submodules and delete any existing files if submodules are present
+      if (!(await git.submoduleStatus())){
+        remove = true
+      }
+
       // Clean
       if (clean) {
         core.startGroup('Cleaning the repository')