diff --git a/java_codebase_rag/pipeline.py b/java_codebase_rag/pipeline.py
index 83262c69..bc2d172e 100644
--- a/java_codebase_rag/pipeline.py
+++ b/java_codebase_rag/pipeline.py
@@ -128,6 +128,10 @@ def run_cocoindex_update(
             stdout="",
             stderr=f"java_index_flow_lancedb.py not found under {bd}",
         )
+    # Set CocoIndex concurrency limits to prevent "too many open files" error
+    # See: https://github.com/HumanBean17/java-codebase-rag/issues/293
+    env = env.copy()
+    env.setdefault("COCOINDEX_SOURCE_MAX_INFLIGHT_ROWS", "256")
     cmd: list[str] = [str(exe), "update", COCOINDEX_TARGET]
     if full_reprocess:
         cmd.extend(["--full-reprocess", "-f"])
diff --git a/server.py b/server.py
index 65f737c8..9dc44adb 100644
--- a/server.py
+++ b/server.py
@@ -162,6 +162,9 @@ def _cocoindex_subprocess_env(project_root: Path) -> dict[str, str]:
     idx = os.environ.get("JAVA_CODEBASE_RAG_INDEX_DIR", "").strip()
     if idx:
         sub_env["JAVA_CODEBASE_RAG_INDEX_DIR"] = str(Path(idx).expanduser().resolve())
+    # Set CocoIndex concurrency limits to prevent "too many open files" error
+    # See: https://github.com/HumanBean17/java-codebase-rag/issues/293
+    sub_env.setdefault("COCOINDEX_SOURCE_MAX_INFLIGHT_ROWS", "256")
     return sub_env