diff --git a/src/pipeline/pipeline_incremental.c b/src/pipeline/pipeline_incremental.c
index c6a2024b5..b89c280f2 100644
--- a/src/pipeline/pipeline_incremental.c
+++ b/src/pipeline/pipeline_incremental.c
@@ -455,6 +455,12 @@ static void persist_hashes(cbm_store_t *store, const char *project, cbm_file_inf
     int current_failed = 0;
     int ms_failed = 0;
 
+    /* Batch all hash upserts in one transaction: N files -> 1 COMMIT under
+     * WAL instead of N autocommit fsyncs (a 10k-file reindex did 10k separate
+     * commits). If BEGIN fails (e.g. store busy), fall back to per-row
+     * autocommit. The partial-failure policy below is unchanged. */
+    bool batched = (cbm_store_begin(store) == CBM_STORE_OK);
+
     /* Current discovery: re-stat to capture any mtime/size that changed
      * during the run, and write fresh hash rows for visited files. */
     for (int i = 0; i < file_count; i++) {
@@ -498,6 +504,10 @@ static void persist_hashes(cbm_store_t *store, const char *project, cbm_file_inf
         }
     }
 
+    if (batched) {
+        (void)cbm_store_commit(store);
+    }
+
     if (current_failed > 0 || ms_failed > 0) {
         cbm_log_warn("incremental.persist_summary", "current_failed", itoa_buf_incr(current_failed),
                      "mode_skipped_failed", itoa_buf_incr(ms_failed));