diff --git a/.changeset/shy-pugs-teach.md b/.changeset/shy-pugs-teach.md
new file mode 100644
index 000000000..c8ff5adfb
--- /dev/null
+++ b/.changeset/shy-pugs-teach.md
@@ -0,0 +1,7 @@
+---
+'@powersync/service-module-mongodb': patch
+'@powersync/service-core': patch
+'@powersync/service-image': patch
+---
+
+Fix MongoDB initial replication with mixed \_id types.
diff --git a/modules/module-mongodb/src/replication/ChangeStream.ts b/modules/module-mongodb/src/replication/ChangeStream.ts
index cc2f230dd..f85de233b 100644
--- a/modules/module-mongodb/src/replication/ChangeStream.ts
+++ b/modules/module-mongodb/src/replication/ChangeStream.ts
@@ -451,6 +451,7 @@ export class ChangeStream {
     while (true) {
       const { docs: docBatch, lastKey } = await nextChunkPromise;
       if (docBatch.length == 0) {
+        // No more data - stop iterating
         break;
       }
 
diff --git a/modules/module-mongodb/src/replication/MongoSnapshotQuery.ts b/modules/module-mongodb/src/replication/MongoSnapshotQuery.ts
index c0ff8dc95..501563dc7 100644
--- a/modules/module-mongodb/src/replication/MongoSnapshotQuery.ts
+++ b/modules/module-mongodb/src/replication/MongoSnapshotQuery.ts
@@ -25,7 +25,18 @@ export class ChunkedSnapshotQuery implements AsyncDisposable {
     let cursor = this.lastCursor;
     let newCursor = false;
     if (cursor == null || cursor.closed) {
-      const filter: mongo.Filter<mongo.Document> = this.lastKey == null ? {} : { _id: { $gt: this.lastKey as any } };
+      // This is subtly but importantly different from doing { _id: { $gt: this.lastKey } }.
+      // If there are separate BSON types of _id, then the form above only returns documents in the same type,
+      // while the $expr form will return all documents with _id greater than the lastKey, matching sort order.
+      // Both forms use indexes efficiently.
+      // For details, see:
+      // https://www.mongodb.com/docs/manual/reference/bson-type-comparison-order/#comparison-sort-order
+      // The $literal is necessary to ensure that the lastKey is treated as a literal value, and doesn't attempt
+      // any parsing as an operator.
+      // Starting in MongoDB 5.0, this filter can use the _id index. Source:
+      // https://www.mongodb.com/docs/manual/release-notes/5.0/#general-aggregation-improvements
+      const filter: mongo.Filter<mongo.Document> =
+        this.lastKey == null ? {} : { $expr: { $gt: ['$_id', { $literal: this.lastKey }] } };
       cursor = this.collection.find(filter, {
         batchSize: this.batchSize,
         readConcern: 'majority',
@@ -38,8 +49,10 @@ export class ChunkedSnapshotQuery implements AsyncDisposable {
     if (!hasNext) {
       this.lastCursor = null;
       if (newCursor) {
+        // We just created a new cursor and it has no results - we have finished the end of the query.
         return { docs: [], lastKey: null };
       } else {
+        // The cursor may have hit the batch limit - retry
         return this.nextChunk();
       }
     }
diff --git a/modules/module-mongodb/test/src/chunked_snapshot.test.ts b/modules/module-mongodb/test/src/chunked_snapshot.test.ts
index a3cd937db..c7c3d653d 100644
--- a/modules/module-mongodb/test/src/chunked_snapshot.test.ts
+++ b/modules/module-mongodb/test/src/chunked_snapshot.test.ts
@@ -59,6 +59,31 @@ function defineBatchTests(factory: TestStorageFactory) {
     });
   });
 
+  test('chunked snapshot (mixed)', async () => {
+    await testChunkedSnapshot({
+      generateId(i) {
+        // Alternatingly return a number, string or nested document.
+        // This caused issues in the past due to comparison operators only checking fields matching the same type.
+        if (i % 3 == 0) {
+          return i;
+        } else if (i % 3 == 1) {
+          return `${i}`;
+        } else {
+          return { n: i };
+        }
+      },
+      idToSqlite(id: number | string) {
+        if (typeof id == 'number') {
+          return BigInt(id);
+        } else if (typeof id == 'string') {
+          return id;
+        } else {
+          return JSON.stringify(id);
+        }
+      }
+    });
+  });
+
   async function testChunkedSnapshot(options: {
     generateId: (i: number) => any;
     idToSqlite?: (id: any) => SqliteJsonValue;