diff --git a/packages/core/src/tools/shell.test.ts b/packages/core/src/tools/shell.test.ts
index d1dfc415b7..78b54fe297 100644
--- a/packages/core/src/tools/shell.test.ts
+++ b/packages/core/src/tools/shell.test.ts
@@ -277,7 +277,7 @@ describe('ShellTool', () => {
 
       const result = await promise;
 
-      const wrappedCommand = `{ my-command & }; __code=$?; pgrep -g 0 >${tmpFile} 2>&1; exit $__code;`;
+      const wrappedCommand = `(\n${'my-command &'}\n); __code=$?; pgrep -g 0 >${tmpFile} 2>&1; exit $__code;`;
       expect(mockShellExecutionService).toHaveBeenCalledWith(
         wrappedCommand,
         tempRootDir,
@@ -295,6 +295,42 @@ describe('ShellTool', () => {
       expect(fs.existsSync(tmpFile)).toBe(false);
     });
 
+    it('should add a space when command ends with a backslash to prevent escaping newline', async () => {
+      const invocation = shellTool.build({ command: 'ls\\' });
+      const promise = invocation.execute(mockAbortSignal);
+      resolveShellExecution();
+      await promise;
+
+      const tmpFile = path.join(os.tmpdir(), 'shell_pgrep_abcdef.tmp');
+      const wrappedCommand = `(\nls\\ \n); __code=$?; pgrep -g 0 >${tmpFile} 2>&1; exit $__code;`;
+      expect(mockShellExecutionService).toHaveBeenCalledWith(
+        wrappedCommand,
+        tempRootDir,
+        expect.any(Function),
+        expect.any(AbortSignal),
+        false,
+        expect.any(Object),
+      );
+    });
+
+    it('should handle trailing comments correctly by placing them on their own line', async () => {
+      const invocation = shellTool.build({ command: 'ls # comment' });
+      const promise = invocation.execute(mockAbortSignal);
+      resolveShellExecution();
+      await promise;
+
+      const tmpFile = path.join(os.tmpdir(), 'shell_pgrep_abcdef.tmp');
+      const wrappedCommand = `(\nls # comment\n); __code=$?; pgrep -g 0 >${tmpFile} 2>&1; exit $__code;`;
+      expect(mockShellExecutionService).toHaveBeenCalledWith(
+        wrappedCommand,
+        tempRootDir,
+        expect.any(Function),
+        expect.any(AbortSignal),
+        false,
+        expect.any(Object),
+      );
+    });
+
     it('should use the provided absolute directory as cwd', async () => {
       const subdir = path.join(tempRootDir, 'subdir');
       const invocation = shellTool.build({
@@ -306,7 +342,7 @@ describe('ShellTool', () => {
       await promise;
 
       const tmpFile = path.join(os.tmpdir(), 'shell_pgrep_abcdef.tmp');
-      const wrappedCommand = `{ ls; }; __code=$?; pgrep -g 0 >${tmpFile} 2>&1; exit $__code;`;
+      const wrappedCommand = `(\n${'ls'}\n); __code=$?; pgrep -g 0 >${tmpFile} 2>&1; exit $__code;`;
       expect(mockShellExecutionService).toHaveBeenCalledWith(
         wrappedCommand,
         subdir,
@@ -331,7 +367,7 @@ describe('ShellTool', () => {
       await promise;
 
       const tmpFile = path.join(os.tmpdir(), 'shell_pgrep_abcdef.tmp');
-      const wrappedCommand = `{ ls; }; __code=$?; pgrep -g 0 >${tmpFile} 2>&1; exit $__code;`;
+      const wrappedCommand = `(\n${'ls'}\n); __code=$?; pgrep -g 0 >${tmpFile} 2>&1; exit $__code;`;
       expect(mockShellExecutionService).toHaveBeenCalledWith(
         wrappedCommand,
         path.join(tempRootDir, 'subdir'),
diff --git a/packages/core/src/tools/shell.ts b/packages/core/src/tools/shell.ts
index 0b4760ccc7..3a70de3ea4 100644
--- a/packages/core/src/tools/shell.ts
+++ b/packages/core/src/tools/shell.ts
@@ -76,6 +76,33 @@ export class ShellToolInvocation extends BaseToolInvocation<
     super(params, messageBus, _toolName, _toolDisplayName);
   }
 
+  /**
+   * Wraps a command in a subshell `()` to capture background process IDs (PIDs) using pgrep.
+   * Uses newlines to prevent breaking heredocs or trailing comments.
+   *
+   * @param command The raw command string to execute.
+   * @param tempFilePath Path to the temporary file where PIDs will be written.
+   * @param isWindows Whether the current platform is Windows (if true, the command is returned as-is).
+   * @returns The wrapped command string.
+   */
+  private wrapCommandForPgrep(
+    command: string,
+    tempFilePath: string,
+    isWindows: boolean,
+  ): string {
+    if (isWindows) {
+      return command;
+    }
+    let trimmed = command.trim();
+    if (!trimmed) {
+      return '';
+    }
+    if (trimmed.endsWith('\\')) {
+      trimmed += ' ';
+    }
+    return `(\n${trimmed}\n); __code=$?; pgrep -g 0 >${tempFilePath} 2>&1; exit $__code;`;
+  }
+
   private getContextualDetails(): string {
     let details = '';
     // append optional [in directory]
@@ -232,14 +259,11 @@ export class ShellToolInvocation extends BaseToolInvocation<
 
     try {
       // pgrep is not available on Windows, so we can't get background PIDs
-      const commandToExecute = isWindows
-        ? strippedCommand
-        : (() => {
-            // wrap command to append subprocess pids (via pgrep) to temporary file
-            let command = strippedCommand.trim();
-            if (!command.endsWith('&')) command += ';';
-            return `{ ${command} }; __code=$?; pgrep -g 0 >${tempFilePath} 2>&1; exit $__code;`;
-          })();
+      const commandToExecute = this.wrapCommandForPgrep(
+        strippedCommand,
+        tempFilePath,
+        isWindows,
+      );
 
       const cwd = this.params.dir_path
         ? path.resolve(this.context.config.getTargetDir(), this.params.dir_path)