diff --git a/.changeset/quiet-indexing-startup.md b/.changeset/quiet-indexing-startup.md
new file mode 100644
index 00000000000..5a0260139b7
--- /dev/null
+++ b/.changeset/quiet-indexing-startup.md
@@ -0,0 +1,5 @@
+---
+"@kilocode/cli": patch
+---
+
+Keep the extension usable on fresh startup when semantic indexing is enabled globally.
diff --git a/packages/opencode/src/kilocode/config/default-plugins.ts b/packages/opencode/src/kilocode/config/default-plugins.ts
index 393226f93e0..ad709dd24e7 100644
--- a/packages/opencode/src/kilocode/config/default-plugins.ts
+++ b/packages/opencode/src/kilocode/config/default-plugins.ts
@@ -1,5 +1,6 @@
 import { createRequire } from "module"
 import type { ConfigPlugin } from "@/config/plugin"
+import { isIndexingPlugin } from "@kilocode/kilo-indexing/detect"
 import { ensureIndexingPlugin, resolveIndexingPlugin } from "@/kilocode/indexing-feature"
 
 type Log = {
@@ -13,17 +14,10 @@ export namespace KilocodeDefaultPlugins {
     cfg: T,
     opts: { disabled: boolean; log?: Log },
   ): T {
-    const before = cfg.plugin ?? []
     const plugin = opts.disabled ? undefined : resolveIndexingPlugin(req, opts.log)
-    const after = ensureIndexingPlugin(before, plugin)
-    if (after.length > before.length) {
-      const added = after[after.length - 1]
-      cfg.plugin_origins = [
-        ...(cfg.plugin_origins ?? []),
-        { spec: added, source: "builtin", scope: "global" as ConfigPlugin.Scope },
-      ]
-    }
-    cfg.plugin = after
+    cfg.plugin = ensureIndexingPlugin(cfg.plugin ?? [], plugin)
+    // Built-in indexing is not loaded through external plugins and must not wait for their setup.
+    cfg.plugin_origins = cfg.plugin_origins?.filter((item) => !isIndexingPlugin(item.spec))
     return cfg
   }
 }
diff --git a/packages/opencode/test/kilocode/config/indexing-default-plugin.test.ts b/packages/opencode/test/kilocode/config/indexing-default-plugin.test.ts
index 122e494f109..7975c9cc842 100644
--- a/packages/opencode/test/kilocode/config/indexing-default-plugin.test.ts
+++ b/packages/opencode/test/kilocode/config/indexing-default-plugin.test.ts
@@ -6,6 +6,9 @@ import { hasIndexingPlugin } from "@kilocode/kilo-indexing/detect"
 import { Account } from "../../../src/account/account"
 import { Auth } from "../../../src/auth"
 import { Config } from "../../../src/config/config"
+import type { ConfigPlugin } from "../../../src/config/plugin"
+import { KilocodeDefaultPlugins } from "../../../src/kilocode/config/default-plugins"
+import { INDEXING_PLUGIN } from "../../../src/kilocode/indexing-feature"
 import * as CrossSpawnSpawner from "@opencode-ai/core/cross-spawn-spawner"
 import { Env } from "../../../src/env"
 import { AppFileSystem } from "@opencode-ai/core/filesystem"
@@ -50,6 +53,28 @@ describe("kilocode default indexing plugin", () => {
     await disposeAllInstances()
   })
 
+  test("injects indexing without registering an external plugin origin", () => {
+    const config: { plugin?: ConfigPlugin.Spec[]; plugin_origins?: ConfigPlugin.Origin[] } = {}
+
+    KilocodeDefaultPlugins.apply(config, { disabled: false })
+
+    expect(hasIndexingPlugin(config.plugin ?? [])).toBe(true)
+    expect(config.plugin_origins).toBeUndefined()
+  })
+
+  test("removes a persisted indexing marker from external plugin origins", () => {
+    const external: ConfigPlugin.Origin = { spec: "global-plugin", source: "global", scope: "global" }
+    const config = {
+      plugin: [INDEXING_PLUGIN, external.spec],
+      plugin_origins: [{ spec: INDEXING_PLUGIN, source: "global", scope: "global" as const }, external],
+    }
+
+    KilocodeDefaultPlugins.apply(config, { disabled: true })
+
+    expect(config.plugin).toEqual([INDEXING_PLUGIN, external.spec])
+    expect(config.plugin_origins).toEqual([external])
+  })
+
   test("does not hard-enable indexing plugin when default plugins are disabled", async () => {
     const prev = process.env["KILO_DISABLE_DEFAULT_PLUGINS"]
     process.env["KILO_DISABLE_DEFAULT_PLUGINS"] = "true"