diff --git a/plugins/techdocs-backend/src/helpers.ts b/plugins/techdocs-backend/src/helpers.ts
index 25d7f593c2..14f4d490ba 100644
--- a/plugins/techdocs-backend/src/helpers.ts
+++ b/plugins/techdocs-backend/src/helpers.ts
@@ -24,6 +24,7 @@ import defaultBranch from 'default-branch';
 import { Entity } from '@backstage/catalog-model';
 import { InputError } from '@backstage/backend-common';
 import { RemoteProtocol } from './techdocs/stages/prepare/types';
+import { Logger } from 'winston';
 
 export type ParsedLocationAnnotation = {
   type: RemoteProtocol;
@@ -110,6 +111,7 @@ export const getGitHubRepositoryTempFolder = async (
 
 export const checkoutGithubRepository = async (
   repoUrl: string,
+  logger: Logger,
 ): Promise<string> => {
   const parsedGitLocation = parseGitUrl(repoUrl);
   const repositoryTmpPath = await getGitHubRepositoryTempFolder(repoUrl);
@@ -119,14 +121,23 @@ export const checkoutGithubRepository = async (
   const token = process.env.GITHUB_PRIVATE_TOKEN || '';
 
   if (fs.existsSync(repositoryTmpPath)) {
-    const repository = await Repository.open(repositoryTmpPath);
-    const currentBranchName = (await repository.getCurrentBranch()).shorthand();
-    await repository.fetch('origin');
-    await repository.mergeBranches(
-      currentBranchName,
-      `origin/${currentBranchName}`,
-    );
-    return repositoryTmpPath;
+    try {
+      const repository = await Repository.open(repositoryTmpPath);
+      const currentBranchName = (
+        await repository.getCurrentBranch()
+      ).shorthand();
+      await repository.fetch('origin');
+      await repository.mergeBranches(
+        currentBranchName,
+        `origin/${currentBranchName}`,
+      );
+      return repositoryTmpPath;
+    } catch (e) {
+      logger.info(
+        `Found error "${e.message}" in cached repository "${repoUrl}" when getting latest changes. Removing cached repository.`,
+      );
+      fs.removeSync(repositoryTmpPath);
+    }
   }
 
   if (user && token) {
@@ -143,8 +154,12 @@ export const checkoutGithubRepository = async (
 
 export const getLastCommitTimestamp = async (
   repositoryUrl: string,
+  logger: Logger,
 ): Promise<number> => {
-  const repositoryLocation = await checkoutGithubRepository(repositoryUrl);
+  const repositoryLocation = await checkoutGithubRepository(
+    repositoryUrl,
+    logger,
+  );
 
   const repository = await Repository.open(repositoryLocation);
   const commit = await repository.getReferenceCommit('HEAD');
diff --git a/plugins/techdocs-backend/src/service/helpers.ts b/plugins/techdocs-backend/src/service/helpers.ts
index 0fc4f41b3d..60c76e6384 100644
--- a/plugins/techdocs-backend/src/service/helpers.ts
+++ b/plugins/techdocs-backend/src/service/helpers.ts
@@ -110,7 +110,7 @@ export class DocsBuilder {
 
     // Should probably be broken out and handled per type later. Doing this for now since we only support github age checks
     if (type === 'github') {
-      const lastCommit = await getLastCommitTimestamp(target);
+      const lastCommit = await getLastCommitTimestamp(target, this.logger);
       const storageTimeStamp = buildMetadataStorage.getTimestamp();
 
       // Check if documentation source is newer than what we have
diff --git a/plugins/techdocs-backend/src/techdocs/stages/prepare/dir.ts b/plugins/techdocs-backend/src/techdocs/stages/prepare/dir.ts
index a9eda943c6..5fd4abb4bd 100644
--- a/plugins/techdocs-backend/src/techdocs/stages/prepare/dir.ts
+++ b/plugins/techdocs-backend/src/techdocs/stages/prepare/dir.ts
@@ -43,7 +43,10 @@ export class DirectoryPreparer implements PreparerBase {
     switch (type) {
       case 'github': {
         const parsedGitLocation = parseGitUrl(target);
-        const repoLocation = await checkoutGithubRepository(target);
+        const repoLocation = await checkoutGithubRepository(
+          target,
+          this.logger,
+        );
 
         return path.dirname(
           path.join(repoLocation, parsedGitLocation.filepath),
diff --git a/plugins/techdocs-backend/src/techdocs/stages/prepare/github.ts b/plugins/techdocs-backend/src/techdocs/stages/prepare/github.ts
index 7b9fc7fbe2..03b0adcb88 100644
--- a/plugins/techdocs-backend/src/techdocs/stages/prepare/github.ts
+++ b/plugins/techdocs-backend/src/techdocs/stages/prepare/github.ts
@@ -43,7 +43,7 @@ export class GithubPreparer implements PreparerBase {
     }
 
     try {
-      const repoPath = await checkoutGithubRepository(target);
+      const repoPath = await checkoutGithubRepository(target, this.logger);
 
       const parsedGitLocation = parseGitUrl(target);
       return path.join(repoPath, parsedGitLocation.filepath);