diff --git a/packages/backend/src/connectionManager.ts b/packages/backend/src/connectionManager.ts
index 456c5d15..4fcc4113 100644
--- a/packages/backend/src/connectionManager.ts
+++ b/packages/backend/src/connectionManager.ts
@@ -1,6 +1,6 @@
 import { Connection, ConnectionSyncStatus, PrismaClient, Prisma } from "@sourcebot/db";
 import { Job, Queue, Worker } from 'bullmq';
-import { AppContext, Settings, WithRequired } from "./types.js";
+import { Settings, WithRequired } from "./types.js";
 import { ConnectionConfig } from "@sourcebot/schemas/v3/connection.type";
 import { createLogger } from "./logger.js";
 import os from 'os';
@@ -10,6 +10,7 @@ import { getGitHubReposFromConfig } from "./github.js";
 
 interface IConnectionManager {
     scheduleConnectionSync: (connection: Connection) => Promise<void>;
+    registerPollingCallback: () => void;
     dispose: () => void;
 }
 
@@ -28,14 +29,13 @@ export class ConnectionManager implements IConnectionManager {
 
     constructor(
         private db: PrismaClient,
-        settings: Settings,
+        private settings: Settings,
         redis: Redis,
-        private context: AppContext,
     ) {
         const numCores = os.cpus().length;
         this.worker = new Worker(QUEUE_NAME, this.runSyncJob.bind(this), {
             connection: redis,
-            concurrency: numCores * settings.configSyncConcurrencyMultiple,
+            concurrency: numCores * this.settings.configSyncConcurrencyMultiple,
         });
         this.worker.on('completed', this.onSyncJobCompleted.bind(this));
         this.worker.on('failed', this.onSyncJobFailed.bind(this));
@@ -61,6 +61,19 @@ export class ConnectionManager implements IConnectionManager {
         });
     }
 
+    public async registerPollingCallback() {
+        setInterval(async () => {
+            const connections = await this.db.connection.findMany({
+                where: {
+                    syncStatus: ConnectionSyncStatus.SYNC_NEEDED,
+                }
+            });
+            for (const connection of connections) {
+                await this.scheduleConnectionSync(connection);
+            }
+        }, this.settings.resyncConnectionPollingIntervalMs);
+    }
+
     private async runSyncJob(job: Job<JobPayload>) {
         const { config, orgId } = job.data;
         // @note: We aren't actually doing anything with this atm.
diff --git a/packages/backend/src/constants.ts b/packages/backend/src/constants.ts
index 407ec462..bbc5e2eb 100644
--- a/packages/backend/src/constants.ts
+++ b/packages/backend/src/constants.ts
@@ -8,6 +8,7 @@ export const DEFAULT_SETTINGS: Settings = {
     autoDeleteStaleRepos: true,
     reindexIntervalMs: 1000 * 60,
     resyncConnectionPollingIntervalMs: 1000,
+    reindexRepoPollingInternvalMs: 1000,
     indexConcurrencyMultiple: 3,
     configSyncConcurrencyMultiple: 3,
 }
\ No newline at end of file
diff --git a/packages/backend/src/main.ts b/packages/backend/src/main.ts
index d74e6d93..c6245178 100644
--- a/packages/backend/src/main.ts
+++ b/packages/backend/src/main.ts
@@ -1,120 +1,14 @@
-import { ConnectionSyncStatus, PrismaClient, Repo, RepoIndexingStatus, RepoToConnection, Connection } from '@sourcebot/db';
-import { existsSync } from 'fs';
-import { cloneRepository, fetchRepository } from "./git.js";
+import { PrismaClient } from '@sourcebot/db';
 import { createLogger } from "./logger.js";
-import { captureEvent } from "./posthog.js";
 import { AppContext } from "./types.js";
-import { getRepoPath, getTokenFromConfig, measure } from "./utils.js";
-import { indexGitRepository } from "./zoekt.js";
 import { DEFAULT_SETTINGS } from './constants.js';
-import { Queue, Worker, Job } from 'bullmq';
 import { Redis } from 'ioredis';
-import * as os from 'os';
 import { ConnectionManager } from './connectionManager.js';
-import { ConnectionConfig } from '@sourcebot/schemas/v3/connection.type';
+import { RepoManager } from './repoManager.js';
 
 const logger = createLogger('main');
 
-type RepoWithConnections = Repo & { connections: (RepoToConnection & { connection: Connection})[] };
-
-// TODO: do this better? ex: try using the tokens from all the connections 
-// We can no longer use repo.cloneUrl directly since it doesn't contain the token for security reasons. As a result, we need to
-// fetch the token here using the connections from the repo. Multiple connections could be referencing this repo, and each
-// may have their own token. This method will just pick the first connection that has a token (if one exists) and uses that. This
-// may technically cause syncing to fail if that connection's token just so happens to not have access to the repo it's referrencing.
-const getTokenForRepo = async (repo: RepoWithConnections, db: PrismaClient) => {
-    const repoConnections = repo.connections;
-    if (repoConnections.length === 0) {
-        logger.error(`Repo ${repo.id} has no connections`);
-        return;
-    }
-
-    let token: string | undefined;
-    for (const repoConnection of repoConnections) {
-        const connection = repoConnection.connection;
-        const config = connection.config as unknown as ConnectionConfig;
-        if (config.token) {
-            token = await getTokenFromConfig(config.token, connection.orgId, db);
-            if (token) {
-                break;
-            }
-        }
-    }
-
-    return token;
-}
-
-const syncGitRepository = async (repo: RepoWithConnections, ctx: AppContext, db: PrismaClient) => {
-    let fetchDuration_s: number | undefined = undefined;
-    let cloneDuration_s: number | undefined = undefined;
-
-    const repoPath = getRepoPath(repo, ctx);
-    const metadata = repo.metadata as Record<string, string>;
-
-    if (existsSync(repoPath)) {
-        logger.info(`Fetching ${repo.id}...`);
-
-        const { durationMs } = await measure(() => fetchRepository(repoPath, ({ method, stage, progress }) => {
-            logger.info(`git.${method} ${stage} stage ${progress}% complete for ${repo.id}`)
-        }));
-        fetchDuration_s = durationMs / 1000;
-
-        process.stdout.write('\n');
-        logger.info(`Fetched ${repo.name} in ${fetchDuration_s}s`);
-
-    } else {
-        logger.info(`Cloning ${repo.id}...`);
-
-        const token = await getTokenForRepo(repo, db);
-        let cloneUrl = repo.cloneUrl;
-        if (token) {
-            const url = new URL(cloneUrl);
-            url.username = token;
-            cloneUrl = url.toString();
-        }
-
-        const { durationMs } = await measure(() => cloneRepository(cloneUrl, repoPath, metadata, ({ method, stage, progress }) => {
-            logger.info(`git.${method} ${stage} stage ${progress}% complete for ${repo.id}`)
-        }));
-        cloneDuration_s = durationMs / 1000;
-
-        process.stdout.write('\n');
-        logger.info(`Cloned ${repo.id} in ${cloneDuration_s}s`);
-    }
-
-    logger.info(`Indexing ${repo.id}...`);
-    const { durationMs } = await measure(() => indexGitRepository(repo, ctx));
-    const indexDuration_s = durationMs / 1000;
-    logger.info(`Indexed ${repo.id} in ${indexDuration_s}s`);
-
-    return {
-        fetchDuration_s,
-        cloneDuration_s,
-        indexDuration_s,
-    }
-}
-
-async function addReposToQueue(db: PrismaClient, queue: Queue, repos: Repo[]) {
-    for (const repo of repos) {
-        await db.$transaction(async (tx) => {
-            await tx.repo.update({
-                where: { id: repo.id },
-                data: { repoIndexingStatus: RepoIndexingStatus.IN_INDEX_QUEUE },
-            });
-
-            // Add the job to the queue
-            await queue.add('indexJob', repo);
-            logger.info(`Added job to queue for repo ${repo.id}`);
-        }).catch((err: unknown) => {
-            logger.error(`Failed to add job to queue for repo ${repo.id}: ${err}`);
-        });
-    }
-}
-
 export const main = async (db: PrismaClient, context: AppContext) => {
-    /////////////////////////////
-    // Init Redis
-    /////////////////////////////
     const redis = new Redis({
         host: 'localhost',
         port: 6379,
@@ -128,99 +22,9 @@ export const main = async (db: PrismaClient, context: AppContext) => {
         process.exit(1);
     });
 
-    const connectionManager = new ConnectionManager(db, DEFAULT_SETTINGS, redis, context);
-    setInterval(async () => {
-        const connections = await db.connection.findMany({
-            where: {
-                syncStatus: ConnectionSyncStatus.SYNC_NEEDED,
-            }
-        });
-        for (const connection of connections) {
-            await connectionManager.scheduleConnectionSync(connection);
-        }
-    }, DEFAULT_SETTINGS.resyncConnectionPollingIntervalMs);
-    
-    /////////////////////////
-    // Setup repo indexing
-    /////////////////////////
-    const indexQueue = new Queue('indexQueue');
-
-    const numCores = os.cpus().length;
-    const numWorkers = numCores * DEFAULT_SETTINGS.indexConcurrencyMultiple;
-    logger.info(`Detected ${numCores} cores. Setting repo index max concurrency to ${numWorkers}`);
-    const worker = new Worker('indexQueue', async (job: Job) => {
-        const repo = job.data as RepoWithConnections;
-
-        let indexDuration_s: number | undefined;
-        let fetchDuration_s: number | undefined;
-        let cloneDuration_s: number | undefined;
-
-        const stats = await syncGitRepository(repo, context, db);
-        indexDuration_s = stats.indexDuration_s;
-        fetchDuration_s = stats.fetchDuration_s;
-        cloneDuration_s = stats.cloneDuration_s;
-
-        captureEvent('repo_synced', {
-            vcs: 'git',
-            codeHost: repo.external_codeHostType,
-            indexDuration_s,
-            fetchDuration_s,
-            cloneDuration_s,
-        });
-
-        await db.repo.update({
-            where: {
-                id: repo.id,
-            },
-            data: {
-                indexedAt: new Date(),
-                repoIndexingStatus: RepoIndexingStatus.INDEXED,
-            }
-        });
-    }, { connection: redis, concurrency: numWorkers });
-
-    worker.on('completed', (job: Job) => {
-        logger.info(`Job ${job.id} completed`);
-    });
-    worker.on('failed', async (job: Job | undefined, err: unknown) => {
-        logger.info(`Job failed with error: ${err}`);
-        if (job) {
-            await db.repo.update({
-                where: {
-                    id: job.data.id,
-                },
-                data: {
-                    repoIndexingStatus: RepoIndexingStatus.FAILED,
-                }
-            })
-        }
-    });
-
-    // Repo indexing loop
-    while (true) {
-        const thresholdDate = new Date(Date.now() - DEFAULT_SETTINGS.reindexIntervalMs);
-        const repos = await db.repo.findMany({
-            where: {
-                repoIndexingStatus: {
-                    notIn: [RepoIndexingStatus.IN_INDEX_QUEUE, RepoIndexingStatus.FAILED]
-                },
-                OR: [
-                    { indexedAt: null },
-                    { indexedAt: { lt: thresholdDate } },
-                    { repoIndexingStatus: RepoIndexingStatus.NEW }
-                ]
-            },
-            include: {
-                connections: {
-                    include: {
-                        connection: true
-                    }
-                }
-            }
-        });
-        addReposToQueue(db, indexQueue, repos);
-
+    const connectionManager = new ConnectionManager(db, DEFAULT_SETTINGS, redis);
+    connectionManager.registerPollingCallback();
 
-        await new Promise(resolve => setTimeout(resolve, 1000));
-    }
+    const repoManager = new RepoManager(db, DEFAULT_SETTINGS, redis, context);
+    repoManager.blockingPollLoop();
 }
diff --git a/packages/backend/src/repoManager.ts b/packages/backend/src/repoManager.ts
new file mode 100644
index 00000000..0012b426
--- /dev/null
+++ b/packages/backend/src/repoManager.ts
@@ -0,0 +1,276 @@
+import { Job, Queue, Worker } from 'bullmq';
+import { Redis } from 'ioredis';
+import { createLogger } from "./logger.js";
+import { Connection, PrismaClient, Repo, RepoToConnection, RepoIndexingStatus } from "@sourcebot/db";
+import { ConnectionConfig } from '@sourcebot/schemas/v3/connection.type';
+import { AppContext, Settings } from "./types.js";
+import { captureEvent } from "./posthog.js";
+import { getRepoPath, getTokenFromConfig, measure, getShardPrefix } from "./utils.js";
+import { cloneRepository, fetchRepository } from "./git.js";
+import { existsSync, rmSync, readdirSync } from 'fs';
+import { indexGitRepository } from "./zoekt.js";
+import os from 'os';
+
+interface IRepoManager {
+    blockingPollLoop: () => void;
+    scheduleRepoIndexing: (repo: RepoWithConnections) => Promise<void>;
+    dispose: () => void;
+}
+
+const QUEUE_NAME = 'repoIndexingQueue';
+
+type RepoWithConnections = Repo & { connections: (RepoToConnection & { connection: Connection})[] };
+type JobPayload = {
+    repo: RepoWithConnections,
+}
+
+export class RepoManager implements IRepoManager {
+    private queue = new Queue<JobPayload>(QUEUE_NAME);
+    private worker: Worker;
+    private logger = createLogger('RepoManager');
+
+    constructor(
+        private db: PrismaClient,
+        private settings: Settings,
+        redis: Redis,
+        private ctx: AppContext,
+    ) {
+        const numCores = os.cpus().length;
+        this.worker = new Worker(QUEUE_NAME, this.runIndexJob.bind(this), {
+            connection: redis,
+            concurrency: numCores * this.settings.indexConcurrencyMultiple,
+        });
+        this.worker.on('completed', this.onIndexJobCompleted.bind(this));
+        this.worker.on('failed', this.onIndexJobFailed.bind(this));
+    }
+
+    public async blockingPollLoop() {
+        while(true) {
+            this.fetchAndScheduleRepoIndexing();
+            this.garbageCollectRepo();
+
+            await new Promise(resolve => setTimeout(resolve, this.settings.reindexRepoPollingInternvalMs));
+        }
+    }
+
+    public async scheduleRepoIndexing(repo: RepoWithConnections) {
+        await this.db.$transaction(async (tx) => {
+            await tx.repo.update({
+                where: { id: repo.id },
+                data: { repoIndexingStatus: RepoIndexingStatus.IN_INDEX_QUEUE },
+            });
+
+            await this.queue.add('repoIndexJob', {
+                repo
+            });
+            this.logger.info(`Added job to queue for repo ${repo.id}`);
+        }).catch((err: unknown) => {
+            this.logger.error(`Failed to add job to queue for repo ${repo.id}: ${err}`);
+        });
+    }
+
+    private async fetchAndScheduleRepoIndexing() {
+        const thresholdDate = new Date(Date.now() - this.settings.reindexIntervalMs);
+        const repos = await this.db.repo.findMany({
+            where: {
+                repoIndexingStatus: {
+                    notIn: [RepoIndexingStatus.IN_INDEX_QUEUE, RepoIndexingStatus.FAILED]
+                },
+                OR: [
+                    { indexedAt: null },
+                    { indexedAt: { lt: thresholdDate } },
+                    { repoIndexingStatus: RepoIndexingStatus.NEW }
+                ]
+            },
+            include: {
+                connections: {
+                    include: {
+                        connection: true
+                    }
+                }
+            }
+        });
+
+        for (const repo of repos) {
+            await this.scheduleRepoIndexing(repo);
+        } 
+    }
+
+    private async garbageCollectRepo() {
+        const reposWithNoConnections = await this.db.repo.findMany({
+            where: {
+                repoIndexingStatus: { notIn: [RepoIndexingStatus.IN_INDEX_QUEUE, RepoIndexingStatus.INDEXING] }, // we let the job finish for now so we don't need to worry about cancelling
+                connections: {
+                    none: {}
+                }
+            }
+        });
+
+        for (const repo of reposWithNoConnections) {
+            this.logger.info(`Garbage collecting repo with no connections: ${repo.id}`);
+
+            // delete cloned repo
+            const repoPath = getRepoPath(repo, this.ctx);
+            if(existsSync(repoPath)) {
+                this.logger.info(`Deleting repo directory ${repoPath}`);
+                rmSync(repoPath, { recursive: true, force: true });
+            }
+
+            // delete shards
+            const shardPrefix = getShardPrefix(repo.orgId, repo.id);
+            const files = readdirSync(this.ctx.indexPath).filter(file => file.startsWith(shardPrefix));
+            for (const file of files) {
+                const filePath = `${this.ctx.indexPath}/${file}`;
+                this.logger.info(`Deleting shard file ${filePath}`);
+                rmSync(filePath);
+            }
+        }
+
+        await this.db.repo.deleteMany({
+            where: {
+                id: {
+                    in: reposWithNoConnections.map(repo => repo.id)
+                }
+            }
+        });
+    }
+
+    // TODO: do this better? ex: try using the tokens from all the connections 
+    // We can no longer use repo.cloneUrl directly since it doesn't contain the token for security reasons. As a result, we need to
+    // fetch the token here using the connections from the repo. Multiple connections could be referencing this repo, and each
+    // may have their own token. This method will just pick the first connection that has a token (if one exists) and uses that. This
+    // may technically cause syncing to fail if that connection's token just so happens to not have access to the repo it's referrencing.
+    private async getTokenForRepo(repo: RepoWithConnections, db: PrismaClient) {
+        const repoConnections = repo.connections;
+        if (repoConnections.length === 0) {
+            this.logger.error(`Repo ${repo.id} has no connections`);
+            return;
+        }
+
+        let token: string | undefined;
+        for (const repoConnection of repoConnections) {
+            const connection = repoConnection.connection;
+            const config = connection.config as unknown as ConnectionConfig;
+            if (config.token) {
+                token = await getTokenFromConfig(config.token, connection.orgId, db);
+                if (token) {
+                    break;
+                }
+            }
+        }
+
+        return token;
+    }
+
+    private async syncGitRepository(repo: RepoWithConnections) {
+        let fetchDuration_s: number | undefined = undefined;
+        let cloneDuration_s: number | undefined = undefined;
+    
+        const repoPath = getRepoPath(repo, this.ctx);
+        const metadata = repo.metadata as Record<string, string>;
+    
+        if (existsSync(repoPath)) {
+            this.logger.info(`Fetching ${repo.id}...`);
+    
+            const { durationMs } = await measure(() => fetchRepository(repoPath, ({ method, stage, progress }) => {
+                this.logger.info(`git.${method} ${stage} stage ${progress}% complete for ${repo.id}`)
+            }));
+            fetchDuration_s = durationMs / 1000;
+    
+            process.stdout.write('\n');
+            this.logger.info(`Fetched ${repo.name} in ${fetchDuration_s}s`);
+    
+        } else {
+            this.logger.info(`Cloning ${repo.id}...`);
+    
+            const token = await this.getTokenForRepo(repo, this.db);
+            let cloneUrl = repo.cloneUrl;
+            if (token) {
+                const url = new URL(cloneUrl);
+                url.username = token;
+                cloneUrl = url.toString();
+            }
+    
+            const { durationMs } = await measure(() => cloneRepository(cloneUrl, repoPath, metadata, ({ method, stage, progress }) => {
+                this.logger.info(`git.${method} ${stage} stage ${progress}% complete for ${repo.id}`)
+            }));
+            cloneDuration_s = durationMs / 1000;
+    
+            process.stdout.write('\n');
+            this.logger.info(`Cloned ${repo.id} in ${cloneDuration_s}s`);
+        }
+    
+        this.logger.info(`Indexing ${repo.id}...`);
+        const { durationMs } = await measure(() => indexGitRepository(repo, this.ctx));
+        const indexDuration_s = durationMs / 1000;
+        this.logger.info(`Indexed ${repo.id} in ${indexDuration_s}s`);
+    
+        return {
+            fetchDuration_s,
+            cloneDuration_s,
+            indexDuration_s,
+        }
+    }
+
+    private async runIndexJob(job: Job<JobPayload>) {
+        const repo = job.data.repo as RepoWithConnections;
+        await this.db.repo.update({
+            where: {
+                id: repo.id,
+            },
+            data: {
+                repoIndexingStatus: RepoIndexingStatus.INDEXING,
+            }
+        });
+
+        let indexDuration_s: number | undefined;
+        let fetchDuration_s: number | undefined;
+        let cloneDuration_s: number | undefined;
+
+        const stats = await this.syncGitRepository(repo);
+        indexDuration_s = stats.indexDuration_s;
+        fetchDuration_s = stats.fetchDuration_s;
+        cloneDuration_s = stats.cloneDuration_s;
+
+        captureEvent('repo_synced', {
+            vcs: 'git',
+            codeHost: repo.external_codeHostType,
+            indexDuration_s,
+            fetchDuration_s,
+            cloneDuration_s,
+        });
+    }
+    
+    private async onIndexJobCompleted(job: Job<JobPayload>) {
+        this.logger.info(`Repo index job ${job.id} completed`);
+    
+        await this.db.repo.update({
+            where: {
+                id: job.data.repo.id,
+            },
+            data: {
+                indexedAt: new Date(),
+                repoIndexingStatus: RepoIndexingStatus.INDEXED,
+            }
+        });
+    }
+
+    private async onIndexJobFailed(job: Job<JobPayload> | undefined, err: unknown) {
+        this.logger.info(`Repo index job failed with error: ${err}`);
+        if (job) {
+            await this.db.repo.update({
+                where: {
+                    id: job.data.repo.id,
+                },
+                data: {
+                    repoIndexingStatus: RepoIndexingStatus.FAILED,
+                }
+            })
+        }
+    }
+
+    public async dispose() {
+        this.worker.close();
+        this.queue.close();
+    }
+}
\ No newline at end of file
diff --git a/packages/backend/src/types.ts b/packages/backend/src/types.ts
index 71d8fff8..ce44b5dc 100644
--- a/packages/backend/src/types.ts
+++ b/packages/backend/src/types.ts
@@ -74,6 +74,10 @@ export type Settings = {
      * The polling rate (in milliseconds) at which the db should be checked for connections that need to be re-synced.
      */
     resyncConnectionPollingIntervalMs: number;
+    /**
+     * The polling rate (in milliseconds) at which the db should be checked for repos that should be re-indexed.
+     */
+    reindexRepoPollingInternvalMs: number;
     /**
      * The multiple of the number of CPUs to use for indexing.
      */
diff --git a/packages/backend/src/utils.ts b/packages/backend/src/utils.ts
index f85ea10a..b6ba1091 100644
--- a/packages/backend/src/utils.ts
+++ b/packages/backend/src/utils.ts
@@ -159,4 +159,8 @@ export const arraysEqualShallow = <T>(a?: readonly T[], b?: readonly T[]) => {
 
 export const getRepoPath = (repo: Repo, ctx: AppContext) => {
     return path.join(ctx.reposPath, repo.id.toString());
+}
+
+export const getShardPrefix = (orgId: number, repoId: number) => {
+    return `${orgId}_${repoId}`;
 }
\ No newline at end of file
diff --git a/packages/backend/src/zoekt.ts b/packages/backend/src/zoekt.ts
index 088ae03c..0c4727d0 100644
--- a/packages/backend/src/zoekt.ts
+++ b/packages/backend/src/zoekt.ts
@@ -3,6 +3,7 @@ import { AppContext, LocalRepository, Settings } from "./types.js";
 import { Repo } from "@sourcebot/db";
 import { getRepoPath } from "./utils.js";
 import { DEFAULT_SETTINGS } from "./constants.js";
+import { getShardPrefix } from "./utils.js";
 
 const ALWAYS_EXCLUDED_DIRS = ['.git', '.hg', '.svn'];
 
@@ -11,7 +12,7 @@ export const indexGitRepository = async (repo: Repo, ctx: AppContext) => {
         'HEAD'
     ];
     
-    const shardPrefix = `${repo.orgId}_${repo.id}`;
+    const shardPrefix = getShardPrefix(repo.orgId, repo.id);
     const repoPath = getRepoPath(repo, ctx);
     const command = `zoekt-git-index -allow_missing_branches -index ${ctx.indexPath} -file_limit ${DEFAULT_SETTINGS.maxFileSize} -branches ${revisions.join(',')} -tenant_id ${repo.orgId} -shard_prefix ${shardPrefix} ${repoPath}`;