diff --git a/packages/cli/src/nonInteractive/session.test.ts b/packages/cli/src/nonInteractive/session.test.ts
index 697db77486d..77aaa26f65e 100644
--- a/packages/cli/src/nonInteractive/session.test.ts
+++ b/packages/cli/src/nonInteractive/session.test.ts
@@ -77,6 +77,7 @@ function createConfig(overrides: ConfigOverrides = {}): Config {
     getDebugMode: () => false,
     getApprovalMode: () => 'auto',
     getOutputFormat: () => 'stream-json',
+    getWarnings: () => [],
     initialize: vi.fn(),
     waitForMcpReady: vi.fn().mockResolvedValue(undefined),
     getMonitorRegistry: () => mockMonitorRegistry,
@@ -330,6 +331,30 @@ describe('runNonInteractiveStreamJson', () => {
     expect(mockDispatcher.dispatch).toHaveBeenCalledWith(initRequest);
   });
 
+  it('writes only warnings produced during deferred initialization to stderr', async () => {
+    const warnings = ['Warning: already emitted before stream-json startup'];
+    const stderrWrite = vi.spyOn(process.stderr, 'write').mockReturnValue(true);
+    config = createConfig({
+      getWarnings: () => warnings,
+      initialize: vi.fn().mockImplementation(async () => {
+        warnings.push('Warning: emitted during stream-json initialization');
+      }),
+    });
+
+    mockInputReader.read = async function* () {
+      yield createControlRequest('initialize');
+    };
+
+    await runNonInteractiveStreamJson(config, '');
+
+    expect(stderrWrite).toHaveBeenCalledWith(
+      'Warning: emitted during stream-json initialization\n',
+    );
+    expect(stderrWrite).not.toHaveBeenCalledWith(
+      'Warning: already emitted before stream-json startup\n',
+    );
+  });
+
   it('processes user message when received as first message', async () => {
     const userMessage = createUserMessage('Hello world');
 
diff --git a/packages/cli/src/nonInteractive/session.ts b/packages/cli/src/nonInteractive/session.ts
index 82cf64159b6..f2fafd326d6 100644
--- a/packages/cli/src/nonInteractive/session.ts
+++ b/packages/cli/src/nonInteractive/session.ts
@@ -155,6 +155,10 @@ class Session {
     debugLogger.debug('[Session] Initializing config');
 
     try {
+      // gemini.tsx has already emitted warnings known before stream-json
+      // initialization starts. Keep that snapshot so only warnings produced
+      // by the deferred initialize() call are written here.
+      const emittedWarnings = new Set(this.config.getWarnings());
       // Bracket `config.initialize()` with the same profiler checkpoints
       // the non-stream-json branch in `gemini.tsx` uses so the
       // `config_initialize_dur` derived phase shows up in stream-json
@@ -166,6 +170,11 @@ class Session {
       profileCheckpoint('config_initialize_start');
       await this.config.initialize(options);
       profileCheckpoint('config_initialize_end');
+      for (const warning of this.config.getWarnings()) {
+        if (emittedWarnings.has(warning)) continue;
+        emittedWarnings.add(warning);
+        process.stderr.write(`${warning}\n`);
+      }
       // Stream-json sessions feed prompts straight to the model after init.
       // Under progressive MCP availability `initialize()` returns before
       // MCP servers settle, so we must explicitly await discovery here —