diff --git a/packages/cli/src/nonInteractiveCli.test.ts b/packages/cli/src/nonInteractiveCli.test.ts
index 938eb4e7..3e4ce037 100644
--- a/packages/cli/src/nonInteractiveCli.test.ts
+++ b/packages/cli/src/nonInteractiveCli.test.ts
@@ -70,6 +70,7 @@ describe('runNonInteractive', () => {
       getIdeMode: vi.fn().mockReturnValue(false),
       getFullContext: vi.fn().mockReturnValue(false),
       getContentGeneratorConfig: vi.fn().mockReturnValue({}),
+      getDebugMode: vi.fn().mockReturnValue(false),
     } as unknown as Config;
   });
 
diff --git a/packages/cli/src/nonInteractiveCli.ts b/packages/cli/src/nonInteractiveCli.ts
index 8e573134..8b056a28 100644
--- a/packages/cli/src/nonInteractiveCli.ts
+++ b/packages/cli/src/nonInteractiveCli.ts
@@ -17,28 +17,37 @@ import {
 import { Content, Part, FunctionCall } from '@google/genai';
 
 import { parseAndFormatApiError } from './ui/utils/errorParsing.js';
+import { ConsolePatcher } from './ui/utils/ConsolePatcher.js';
 
 export async function runNonInteractive(
   config: Config,
   input: string,
   prompt_id: string,
 ): Promise<void> {
-  await config.initialize();
-  // Handle EPIPE errors when the output is piped to a command that closes early.
-  process.stdout.on('error', (err: NodeJS.ErrnoException) => {
-    if (err.code === 'EPIPE') {
-      // Exit gracefully if the pipe is closed.
-      process.exit(0);
-    }
+  const consolePatcher = new ConsolePatcher({
+    stderr: true,
+    debugMode: config.getDebugMode(),
   });
 
-  const geminiClient = config.getGeminiClient();
-  const toolRegistry: ToolRegistry = await config.getToolRegistry();
-
-  const abortController = new AbortController();
-  let currentMessages: Content[] = [{ role: 'user', parts: [{ text: input }] }];
-  let turnCount = 0;
   try {
+    await config.initialize();
+    consolePatcher.patch();
+    // Handle EPIPE errors when the output is piped to a command that closes early.
+    process.stdout.on('error', (err: NodeJS.ErrnoException) => {
+      if (err.code === 'EPIPE') {
+        // Exit gracefully if the pipe is closed.
+        process.exit(0);
+      }
+    });
+
+    const geminiClient = config.getGeminiClient();
+    const toolRegistry: ToolRegistry = await config.getToolRegistry();
+
+    const abortController = new AbortController();
+    let currentMessages: Content[] = [
+      { role: 'user', parts: [{ text: input }] },
+    ];
+    let turnCount = 0;
     while (true) {
       turnCount++;
       if (
@@ -133,6 +142,7 @@ export async function runNonInteractive(
     );
     process.exit(1);
   } finally {
+    consolePatcher.cleanup();
     if (isTelemetrySdkInitialized()) {
       await shutdownTelemetry();
     }
diff --git a/packages/cli/src/ui/utils/ConsolePatcher.ts b/packages/cli/src/ui/utils/ConsolePatcher.ts
index 10be3bc7..a429698d 100644
--- a/packages/cli/src/ui/utils/ConsolePatcher.ts
+++ b/packages/cli/src/ui/utils/ConsolePatcher.ts
@@ -8,8 +8,9 @@ import util from 'util';
 import { ConsoleMessageItem } from '../types.js';
 
 interface ConsolePatcherParams {
-  onNewMessage: (message: Omit<ConsoleMessageItem, 'id'>) => void;
+  onNewMessage?: (message: Omit<ConsoleMessageItem, 'id'>) => void;
   debugMode: boolean;
+  stderr?: boolean;
 }
 
 export class ConsolePatcher {
@@ -46,16 +47,22 @@ export class ConsolePatcher {
       originalMethod: (...args: unknown[]) => void,
     ) =>
     (...args: unknown[]) => {
-      if (this.params.debugMode) {
-        originalMethod.apply(console, args);
-      }
+      if (this.params.stderr) {
+        if (type !== 'debug' || this.params.debugMode) {
+          this.originalConsoleError(this.formatArgs(args));
+        }
+      } else {
+        if (this.params.debugMode) {
+          originalMethod.apply(console, args);
+        }
 
-      if (type !== 'debug' || this.params.debugMode) {
-        this.params.onNewMessage({
-          type,
-          content: this.formatArgs(args),
-          count: 1,
-        });
+        if (type !== 'debug' || this.params.debugMode) {
+          this.params.onNewMessage?.({
+            type,
+            content: this.formatArgs(args),
+            count: 1,
+          });
+        }
       }
     };
 }