diff --git a/.agents/decisions.yaml b/.agents/decisions.yaml
index 6de1086..46e9621 100644
--- a/.agents/decisions.yaml
+++ b/.agents/decisions.yaml
@@ -25,4 +25,14 @@ entries:
         escapeQueryString escapes syntax-active characters (context-aware for +/- and &&/||); mid-word hyphens like test-stability stay intact.
         Decision documented so future search work does not re-introduce raw QueryStringQuery usage.
       source: user-requested robustness fix, 2026-09-08
-      date: "2026-09-08"
\ No newline at end of file
+      date: "2026-09-08"
+    - id: dec-004
+      summary: Background indexing with --no-index-on-startup for large stores
+      detail: |-
+        Synchronous indexing on startup blocked server readiness for large knowledge stores.
+        Changed to background goroutine (go idx.IndexAll(resolver)) with ready channel for query synchronization.
+        Added --no-index-on-startup flag to skip indexing entirely; useful when startup delay is unacceptable.
+        Queries block on ready channel until indexing completes; stale data remains available if index has data.
+        readyOnce (sync.Once) prevents double-close panic when NewIndex already closed ready channel.
+      source: GH-25 background indexing, 2026-09-20
+      date: "2026-09-20"
\ No newline at end of file
diff --git a/.agents/subsystems.yaml b/.agents/subsystems.yaml
index cbde413..a259917 100644
--- a/.agents/subsystems.yaml
+++ b/.agents/subsystems.yaml
@@ -32,4 +32,14 @@ entries:
         update_knowledge validates supersedes references an existing ID in the same category and rejects no-op updates.
         Rules surface as a constraints section in list_knowledge output, above regular entries.
       source: code review, 2026-09-08
-      date: "2026-09-08"
\ No newline at end of file
+      date: "2026-09-08"
+    - id: sub-004
+      summary: Background indexing with --no-index-on-startup flag
+      detail: |-
+        IndexAll runs as a goroutine (go idx.IndexAll(resolver)) when --no-index-on-startup is false (default).
+        When --no-index-on-startup is true, indexing is skipped entirely; server starts with stale or empty index.
+        Queries block on ready channel until indexing completes; ready channel closes when IndexAll finishes or if index has stale data.
+        readyOnce (sync.Once) prevents double-close panic if NewIndex already closed ready channel.
+        Useful for large knowledge stores where startup indexing would delay server readiness.
+      source: GH-25 background indexing, 2026-09-20
+      date: "2026-09-20"
\ No newline at end of file
diff --git a/README.md b/README.md
index 6893f61..e222681 100644
--- a/README.md
+++ b/README.md
@@ -174,6 +174,13 @@ General notes:
 - Multi-entry configurations store the search index under `$XDG_STATE_HOME/knowledge-mcp/` (default `~/.local/state/knowledge-mcp/`). Single-flag configurations keep the index inside their own `.agents/` — unless `--store` is set, in which case the index lives at `<store>/.index`.
 - `--index <path>` overrides the index location in all modes.
 
+### Startup Options
+
+`--no-index-on-startup` skips background indexing on startup. The server starts
+immediately with stale or empty index data; queries block until indexing completes
+if no stale data is available. Useful for large knowledge stores where startup
+indexing would delay server readiness.
+
 ## MCP Tools
 
 | Tool | Description |