diff --git a/src/plugins/hook-runner-global.test.ts b/src/plugins/hook-runner-global.test.ts
index 8089feff430..f0901efdf4f 100644
--- a/src/plugins/hook-runner-global.test.ts
+++ b/src/plugins/hook-runner-global.test.ts
@@ -46,4 +46,54 @@ describe("hook-runner-global", () => {
     expect(modC.getGlobalHookRunner()).toBeNull();
     expect(modC.getGlobalPluginRegistry()).toBeNull();
   });
+
+  it("does not replace an existing runner that has typed hooks", async () => {
+    const mod = await importHookRunnerGlobalModule();
+    const registryWithHooks = createMockPluginRegistry([
+      { hookName: "llm_input", handler: vi.fn() },
+    ]);
+    const emptyRegistry = createMockPluginRegistry([]);
+
+    mod.initializeGlobalHookRunner(registryWithHooks);
+    const originalRunner = mod.getGlobalHookRunner();
+    expect(originalRunner?.hasHooks("llm_input")).toBe(true);
+
+    // Second call with empty registry should be a no-op
+    mod.initializeGlobalHookRunner(emptyRegistry);
+    expect(mod.getGlobalHookRunner()).toBe(originalRunner);
+    expect(mod.getGlobalPluginRegistry()).toBe(registryWithHooks);
+    expect(mod.getGlobalHookRunner()?.hasHooks("llm_input")).toBe(true);
+  });
+
+  it("allows replacing a runner that has no typed hooks", async () => {
+    const mod = await importHookRunnerGlobalModule();
+    const emptyRegistry = createMockPluginRegistry([]);
+    const registryWithHooks = createMockPluginRegistry([
+      { hookName: "llm_input", handler: vi.fn() },
+    ]);
+
+    mod.initializeGlobalHookRunner(emptyRegistry);
+    expect(mod.getGlobalHookRunner()?.hasHooks("llm_input")).toBe(false);
+
+    // Second call with hooks should replace
+    mod.initializeGlobalHookRunner(registryWithHooks);
+    expect(mod.getGlobalHookRunner()?.hasHooks("llm_input")).toBe(true);
+    expect(mod.getGlobalPluginRegistry()).toBe(registryWithHooks);
+  });
+
+  it("allows re-initialization after reset", async () => {
+    const mod = await importHookRunnerGlobalModule();
+    const registryA = createMockPluginRegistry([{ hookName: "llm_input", handler: vi.fn() }]);
+    const registryB = createMockPluginRegistry([{ hookName: "llm_output", handler: vi.fn() }]);
+
+    mod.initializeGlobalHookRunner(registryA);
+    expect(mod.getGlobalHookRunner()?.hasHooks("llm_input")).toBe(true);
+
+    mod.resetGlobalHookRunner();
+    expect(mod.getGlobalHookRunner()).toBeNull();
+
+    mod.initializeGlobalHookRunner(registryB);
+    expect(mod.getGlobalHookRunner()?.hasHooks("llm_output")).toBe(true);
+    expect(mod.getGlobalHookRunner()?.hasHooks("llm_input")).toBe(false);
+  });
 });
diff --git a/src/plugins/hook-runner-global.ts b/src/plugins/hook-runner-global.ts
index b2613f3467f..ba7490a560f 100644
--- a/src/plugins/hook-runner-global.ts
+++ b/src/plugins/hook-runner-global.ts
@@ -35,6 +35,14 @@ function getHookRunnerGlobalState(): HookRunnerGlobalState {
  */
 export function initializeGlobalHookRunner(registry: PluginRegistry): void {
   const state = getHookRunnerGlobalState();
+  // Preserve an existing hook runner that has registered hooks.
+  // Subsequent ensureRuntimePluginsLoaded calls (e.g. from non-default agent runs)
+  // may build a fresh registry with fewer/no hooks due to cache key divergence;
+  // replacing the working runner would silently drop all plugin hooks.
+  if (state.hookRunner && state.registry && state.registry.typedHooks.length > 0) {
+    log.debug("hook runner already initialized with hooks; skipping re-initialization");
+    return;
+  }
   state.registry = registry;
   state.hookRunner = createHookRunner(registry, {
     logger: {