diff --git a/rust/lance/src/dataset/mem_wal/write.rs b/rust/lance/src/dataset/mem_wal/write.rs
index 85d0c92e78b..e1314d629e8 100644
--- a/rust/lance/src/dataset/mem_wal/write.rs
+++ b/rust/lance/src/dataset/mem_wal/write.rs
@@ -1339,7 +1339,9 @@ impl ShardWriter {
         )?;
 
         // Background MemTable flush handler — frozen memtable to Lance file.
-        let memtable_handler = MemTableFlushHandler::new(state.clone(), flusher, epoch, stats);
+        // It rebuilds the same secondary indexes on each flushed generation.
+        let memtable_handler =
+            MemTableFlushHandler::new(state.clone(), flusher, epoch, index_configs.to_vec(), stats);
         task_executor.add_handler(
             "memtable_flusher".to_string(),
             Box::new(memtable_handler),
@@ -2135,6 +2137,12 @@ struct MemTableFlushHandler {
     state: Arc<RwLock<WriterState>>,
     flusher: Arc<MemTableFlusher>,
     epoch: u64,
+    /// Secondary index configs to rebuild on each flushed generation. When
+    /// non-empty the handler flushes via [`MemTableFlusher::flush_with_indexes`]
+    /// so queries over flushed generations use index lookups instead of full
+    /// scans — and so vector search's index-only `fast_search` can see the data
+    /// at all.
+    index_configs: Vec<MemIndexConfig>,
     stats: SharedWriteStats,
 }
 
@@ -2143,12 +2151,14 @@ impl MemTableFlushHandler {
         state: Arc<RwLock<WriterState>>,
         flusher: Arc<MemTableFlusher>,
         epoch: u64,
+        index_configs: Vec<MemIndexConfig>,
         stats: SharedWriteStats,
     ) -> Self {
         Self {
             state,
             flusher,
             epoch,
+            index_configs,
             stats,
         }
     }
@@ -2222,9 +2232,24 @@ impl MemTableFlushHandler {
             let covered_wal_entry_position = wal_flushed_position
                 .or_else(|| memtable.frozen_at_wal_entry_position())
                 .unwrap_or(0);
-            self.flusher
-                .flush(&memtable, self.epoch, covered_wal_entry_position)
+            // Rebuild secondary indexes on the flushed generation so later
+            // queries hit an index instead of scanning. Skip the extra
+            // dataset open when there are no indexes to build. The indexed
+            // path's future is boxed to keep this async block's nesting
+            // under the type-layout recursion limit.
+            if self.index_configs.is_empty() {
+                self.flusher
+                    .flush(&memtable, self.epoch, covered_wal_entry_position)
+                    .await
+            } else {
+                Box::pin(self.flusher.flush_with_indexes(
+                    &memtable,
+                    self.epoch,
+                    &self.index_configs,
+                    covered_wal_entry_position,
+                ))
                 .await
+            }
         }
         .await;
 
@@ -2718,6 +2743,101 @@ mod tests {
         writer.close().await.unwrap();
     }
 
+    /// End-to-end check that the background flush handler rebuilds secondary
+    /// indexes on every flushed generation. Before this, the handler flushed
+    /// via plain `flush`, leaving flushed generations unindexed — point
+    /// lookups had to full-scan and vector search's index-only `fast_search`
+    /// couldn't see the data at all.
+    #[tokio::test]
+    async fn test_flushed_generation_is_indexed() {
+        use crate::index::DatasetIndexExt;
+
+        let (store, base_path, base_uri, _temp_dir) = create_local_store().await;
+        let schema = create_test_schema();
+        let shard_id = Uuid::new_v4();
+
+        let config = ShardWriterConfig {
+            shard_id,
+            shard_spec_id: 0,
+            durable_write: false,
+            sync_indexed_write: true,
+            max_wal_buffer_size: 1024 * 1024,
+            max_wal_flush_interval: None,
+            max_memtable_size: 64 * 1024 * 1024,
+            manifest_scan_batch_size: 2,
+            ..Default::default()
+        };
+
+        let index_configs = vec![MemIndexConfig::BTree(BTreeIndexConfig {
+            name: "id_idx".to_string(),
+            field_id: 0,
+            column: "id".to_string(),
+        })];
+
+        let writer = ShardWriter::open(
+            store,
+            base_path,
+            base_uri.clone(),
+            config,
+            schema.clone(),
+            index_configs,
+        )
+        .await
+        .unwrap();
+
+        writer
+            .put(vec![create_test_batch(&schema, 0, 10)])
+            .await
+            .unwrap();
+
+        // Freeze the active memtable and wait until it lands on disk.
+        writer.force_seal_active().await.unwrap();
+        writer.wait_for_flush_drain().await.unwrap();
+
+        // Resolve the flushed generation recorded in the manifest.
+        let manifest = writer.manifest().await.unwrap().unwrap();
+        assert_eq!(
+            manifest.flushed_generations.len(),
+            1,
+            "expected exactly one flushed generation"
+        );
+        let gen_uri = format!(
+            "{}/_mem_wal/{}/{}",
+            base_uri, shard_id, manifest.flushed_generations[0].path
+        );
+
+        // The flushed generation must carry the BTree index built during flush.
+        let dataset = crate::Dataset::open(&gen_uri).await.unwrap();
+        let indices = dataset.load_indices().await.unwrap();
+        assert_eq!(indices.len(), 1, "flushed generation should have one index");
+        assert_eq!(indices[0].name, "id_idx");
+
+        // A PK filter over it must resolve through the index, not a full scan.
+        let mut scan = dataset.scan();
+        scan.filter("id = 5").unwrap();
+        scan.prefilter(true);
+        let plan = scan.create_plan().await.unwrap();
+        crate::utils::test::assert_plan_node_equals(
+            plan,
+            "LanceRead: ...full_filter=id = Int32(5)...
+  ScalarIndexQuery: query=[id = 5]@id_idx(BTree)",
+        )
+        .await
+        .unwrap();
+
+        // And the index returns the correct row.
+        let batch = dataset
+            .scan()
+            .filter("id = 5")
+            .unwrap()
+            .try_into_batch()
+            .await
+            .unwrap();
+        assert_eq!(batch.num_rows(), 1);
+
+        writer.close().await.unwrap();
+    }
+
     /// Test memtable auto-flush triggered by size threshold.
     #[tokio::test]
     async fn test_shard_writer_auto_flush_by_size() {