diff --git a/CHANGELOG.md b/CHANGELOG.md
index ca43800d..56dfc142 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Fixed
 - Fixed issue where certain file and folder names would cause type errors. [#862](https://github.com/sourcebot-dev/sourcebot/pull/862)
 - Fixed token refresh error "Provider config not found or invalid for: x" when a sso is configured using deprecated env vars. [#841](https://github.com/sourcebot-dev/sourcebot/pull/841)
+- Fixed issue where temporary shard files created on index failure were not being cleaned up. [#805](https://github.com/sourcebot-dev/sourcebot/pull/805)
 
 ## [4.10.27] - 2026-02-05
 
diff --git a/packages/backend/src/repoIndexManager.ts b/packages/backend/src/repoIndexManager.ts
index 6237a034..11fc0b94 100644
--- a/packages/backend/src/repoIndexManager.ts
+++ b/packages/backend/src/repoIndexManager.ts
@@ -1,20 +1,19 @@
 import * as Sentry from '@sentry/node';
 import { PrismaClient, Repo, RepoIndexingJobStatus, RepoIndexingJobType } from "@sourcebot/db";
-import { createLogger, Logger } from "@sourcebot/shared";
-import { env, RepoIndexingJobMetadata, repoIndexingJobMetadataSchema, RepoMetadata, repoMetadataSchema, getRepoPath } from '@sourcebot/shared';
+import { createLogger, env, getRepoPath, Logger, RepoIndexingJobMetadata, repoIndexingJobMetadataSchema, RepoMetadata, repoMetadataSchema } from "@sourcebot/shared";
+import { DelayedError, Job, Queue, Worker } from "bullmq";
 import { existsSync } from 'fs';
 import { readdir, rm } from 'fs/promises';
-import { DelayedError, Job, Queue, Worker } from "bullmq";
 import { Redis } from 'ioredis';
-import Redlock, { ExecutionError } from 'redlock';
 import micromatch from 'micromatch';
-import { WORKER_STOP_GRACEFUL_TIMEOUT_MS, INDEX_CACHE_DIR } from './constants.js';
+import Redlock, { ExecutionError } from 'redlock';
+import { INDEX_CACHE_DIR, WORKER_STOP_GRACEFUL_TIMEOUT_MS } from './constants.js';
 import { cloneRepository, fetchRepository, getBranches, getCommitHashForRefName, getLatestCommitTimestamp, getLocalDefaultBranch, getTags, isPathAValidGitRepoRoot, unsetGitConfig, upsertGitConfig } from './git.js';
 import { captureEvent } from './posthog.js';
 import { PromClient } from './promClient.js';
 import { RepoWithConnections, Settings } from "./types.js";
 import { getAuthCredentialsForRepo, getShardPrefix, 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);
@@ -478,9 +477,17 @@ 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);
+    }
+}