diff --git a/packages/backend/src/repoIndexManager.ts b/packages/backend/src/repoIndexManager.ts
index 8e499863..69226935 100644
--- a/packages/backend/src/repoIndexManager.ts
+++ b/packages/backend/src/repoIndexManager.ts
@@ -13,7 +13,7 @@ import { captureEvent } from './posthog.js';
 import { PromClient } from './promClient.js';
 import { RepoWithConnections, Settings } from "./types.js";
 import { getAuthCredentialsForRepo, getShardPrefix, groupmqLifecycleExceptionWrapper, measure, setIntervalAsync } from './utils.js';
-import { indexGitRepository } from './zoekt.js';
+import { cleanupTempShards, indexGitRepository } from './zoekt.js';
 
 const LOG_TAG = 'repo-index-manager';
 const logger = createLogger(LOG_TAG);
@@ -438,9 +438,17 @@ export class RepoIndexManager {
         }
 
         logger.info(`Indexing ${repo.name} (id: ${repo.id})...`);
-        const { durationMs } = await measure(() => indexGitRepository(repo, this.settings, revisions, signal));
-        const indexDuration_s = durationMs / 1000;
-        logger.info(`Indexed ${repo.name} (id: ${repo.id}) in ${indexDuration_s}s`);
+        try {
+            const { durationMs } = await measure(() => indexGitRepository(repo, this.settings, revisions, signal));
+            const indexDuration_s = durationMs / 1000;
+            logger.info(`Indexed ${repo.name} (id: ${repo.id}) in ${indexDuration_s}s`);
+        } catch (error) {
+            // Clean up any temporary shard files left behind by the failed indexing operation.
+            // Zoekt creates .tmp files during indexing which can accumulate if indexing fails repeatedly.
+            logger.warn(`Indexing failed for ${repo.name} (id: ${repo.id}), cleaning up temp shard files...`);
+            await cleanupTempShards(repo);
+            throw error;
+        }
 
         return revisions;
     }
diff --git a/packages/backend/src/zoekt.ts b/packages/backend/src/zoekt.ts
index 27f17d71..ff97d1ce 100644
--- a/packages/backend/src/zoekt.ts
+++ b/packages/backend/src/zoekt.ts
@@ -1,6 +1,7 @@
 import { Repo } from "@sourcebot/db";
 import { createLogger, env, getRepoPath } from "@sourcebot/shared";
 import { exec } from "child_process";
+import { readdir, rm } from "fs/promises";
 import { INDEX_CACHE_DIR } from "./constants.js";
 import { Settings } from "./types.js";
 import { getShardPrefix } from "./utils.js";
@@ -54,3 +55,34 @@ export const indexGitRepository = async (repo: Repo, settings: Settings, revisio
         })
     });
 }
+
+/**
+ * Cleans up temporary shard files left behind by a failed indexing operation.
+ * Zoekt creates temporary files (with `.tmp` suffix) during indexing, which
+ * can be left behind if the indexing process fails or is interrupted.
+ * 
+ * @param repo - The repository whose temp shards should be cleaned up
+ */
+export const cleanupTempShards = async (repo: Repo) => {
+    const shardPrefix = getShardPrefix(repo.orgId, repo.id);
+    
+    try {
+        const files = await readdir(INDEX_CACHE_DIR);
+        const tempFiles = files.filter(file => 
+            file.startsWith(shardPrefix) && file.includes('.tmp')
+        );
+        
+        for (const file of tempFiles) {
+            const filePath = `${INDEX_CACHE_DIR}/${file}`;
+            logger.info(`Cleaning up temp shard file: ${filePath}`);
+            await rm(filePath, { force: true });
+        }
+        
+        if (tempFiles.length > 0) {
+            logger.info(`Cleaned up ${tempFiles.length} temp shard file(s) for repo ${repo.id}`);
+        }
+    } catch (error) {
+        // Log but don't throw - cleanup is best effort
+        logger.warn(`Failed to cleanup temp shards for repo ${repo.id}:`, error);
+    }
+}