diff --git a/.changeset/seven-mangos-sleep.md b/.changeset/seven-mangos-sleep.md
new file mode 100644
index 00000000..e15a4bc1
--- /dev/null
+++ b/.changeset/seven-mangos-sleep.md
@@ -0,0 +1,7 @@
+---
+'@powersync/service-module-mongodb-storage': patch
+'@powersync/service-core': patch
+'@powersync/service-image': patch
+---
+
+[MongoDB Storage] Only compact modified buckets. Add partial index on bucket_state to handle large numbers of buckets when pre-calculating checksums or compacting.
diff --git a/modules/module-mongodb-storage/src/migrations/db/migrations/1760433882550-bucket-state-index2.ts b/modules/module-mongodb-storage/src/migrations/db/migrations/1760433882550-bucket-state-index2.ts
new file mode 100644
index 00000000..e9fd01c6
--- /dev/null
+++ b/modules/module-mongodb-storage/src/migrations/db/migrations/1760433882550-bucket-state-index2.ts
@@ -0,0 +1,34 @@
+import { migrations } from '@powersync/service-core';
+import * as storage from '../../../storage/storage-index.js';
+import { MongoStorageConfig } from '../../../types/types.js';
+
+const INDEX_NAME = 'dirty_buckets';
+
+export const up: migrations.PowerSyncMigrationFunction = async (context) => {
+  const {
+    service_context: { configuration }
+  } = context;
+  const db = storage.createPowerSyncMongo(configuration.storage as MongoStorageConfig);
+
+  try {
+    await db.createBucketStateIndex2();
+  } finally {
+    await db.client.close();
+  }
+};
+
+export const down: migrations.PowerSyncMigrationFunction = async (context) => {
+  const {
+    service_context: { configuration }
+  } = context;
+
+  const db = storage.createPowerSyncMongo(configuration.storage as MongoStorageConfig);
+
+  try {
+    if (await db.bucket_state.indexExists(INDEX_NAME)) {
+      await db.bucket_state.dropIndex(INDEX_NAME);
+    }
+  } finally {
+    await db.client.close();
+  }
+};
diff --git a/modules/module-mongodb-storage/src/storage/implementation/MongoCompactor.ts b/modules/module-mongodb-storage/src/storage/implementation/MongoCompactor.ts
index e81d566c..b1f2deb4 100644
--- a/modules/module-mongodb-storage/src/storage/implementation/MongoCompactor.ts
+++ b/modules/module-mongodb-storage/src/storage/implementation/MongoCompactor.ts
@@ -99,11 +99,19 @@ export class MongoCompactor {
         await this.compactInternal(bucket);
       }
     } else {
-      await this.compactInternal(undefined);
+      await this.compactDirtyBuckets();
     }
   }
 
-  async compactInternal(bucket: string | undefined) {
+  private async compactDirtyBuckets() {
+    for await (let buckets of this.iterateDirtyBuckets()) {
+      for (let bucket of buckets) {
+        await this.compactInternal(bucket);
+      }
+    }
+  }
+
+  private async compactInternal(bucket: string | undefined) {
     const idLimitBytes = this.idLimitBytes;
 
     let currentState: CurrentBucketState | null = null;
@@ -483,6 +491,16 @@ export class MongoCompactor {
    * Subset of compact, only populating checksums where relevant.
    */
   async populateChecksums() {
+    for await (let buckets of this.iterateDirtyBuckets()) {
+      const start = Date.now();
+      logger.info(`Calculating checksums for batch of ${buckets.length} buckets, starting at ${buckets[0]}`);
+
+      await this.updateChecksumsBatch(buckets);
+      logger.info(`Updated checksums for batch of ${buckets.length} buckets in ${Date.now() - start}ms`);
+    }
+  }
+
+  private async *iterateDirtyBuckets(): AsyncGenerator<string[]> {
     // This is updated after each batch
     let lowerBound: BucketStateDocument['_id'] = {
       g: this.group_id,
@@ -500,10 +518,11 @@ export class MongoCompactor {
           $gt: lowerBound,
           $lt: upperBound
         },
-        compacted_state: { $exists: false }
+        // Partial index exists on this
+        'estimate_since_compact.count': { $gt: 0 }
       };
 
-      const bucketsWithoutChecksums = await this.db.bucket_state
+      const dirtyBuckets = await this.db.bucket_state
         .find(filter, {
           projection: {
             _id: 1
@@ -512,19 +531,19 @@ export class MongoCompactor {
             _id: 1
           },
           limit: 5_000,
-          maxTimeMS: MONGO_OPERATION_TIMEOUT_MS
+          maxTimeMS: MONGO_OPERATION_TIMEOUT_MS,
+          // Make sure we use the partial index
+          hint: 'dirty_buckets'
         })
         .toArray();
-      if (bucketsWithoutChecksums.length == 0) {
-        // All done
+
+      if (dirtyBuckets.length == 0) {
         break;
       }
 
-      logger.info(`Calculating checksums for batch of ${bucketsWithoutChecksums.length} buckets`);
-
-      await this.updateChecksumsBatch(bucketsWithoutChecksums.map((b) => b._id.b));
+      yield dirtyBuckets.map((bucket) => bucket._id.b);
 
-      lowerBound = bucketsWithoutChecksums[bucketsWithoutChecksums.length - 1]._id;
+      lowerBound = dirtyBuckets[dirtyBuckets.length - 1]._id;
     }
   }
 
@@ -559,6 +578,10 @@ export class MongoCompactor {
                 count: bucketChecksum.count,
                 checksum: BigInt(bucketChecksum.checksum),
                 bytes: null
+              },
+              estimate_since_compact: {
+                count: 0,
+                bytes: 0
               }
             }
           },
diff --git a/modules/module-mongodb-storage/src/storage/implementation/MongoTestStorageFactoryGenerator.ts b/modules/module-mongodb-storage/src/storage/implementation/MongoTestStorageFactoryGenerator.ts
index 4aa149bf..d85354be 100644
--- a/modules/module-mongodb-storage/src/storage/implementation/MongoTestStorageFactoryGenerator.ts
+++ b/modules/module-mongodb-storage/src/storage/implementation/MongoTestStorageFactoryGenerator.ts
@@ -25,6 +25,7 @@ export const MongoTestStorageFactoryGenerator = (factoryOptions: MongoTestStorag
     // Full migrations are not currently run for tests, so we manually create the important ones
     await db.createCheckpointEventsCollection();
     await db.createBucketStateIndex();
+    await db.createBucketStateIndex2();
 
     return new MongoBucketStorage(db, { slot_name_prefix: 'test_' }, factoryOptions.internalOptions);
   };
diff --git a/modules/module-mongodb-storage/src/storage/implementation/db.ts b/modules/module-mongodb-storage/src/storage/implementation/db.ts
index e6b08352..326d138b 100644
--- a/modules/module-mongodb-storage/src/storage/implementation/db.ts
+++ b/modules/module-mongodb-storage/src/storage/implementation/db.ts
@@ -141,6 +141,19 @@ export class PowerSyncMongo {
       { name: 'bucket_updates', unique: true }
     );
   }
+  /**
+   * Only use in migrations and tests.
+   */
+  async createBucketStateIndex2() {
+    // TODO: Implement a better mechanism to use migrations in tests
+    await this.bucket_state.createIndex(
+      {
+        _id: 1,
+        'estimate_since_compact.count': 1
+      },
+      { name: 'dirty_buckets', partialFilterExpression: { 'estimate_since_compact.count': { $gt: 0 } } }
+    );
+  }
 }
 
 export function createPowerSyncMongo(config: MongoStorageConfig, options?: lib_mongo.MongoConnectionOptions) {