diff --git a/packages/cli/src/ui/components/messages/ToolConfirmationMessage.test.tsx b/packages/cli/src/ui/components/messages/ToolConfirmationMessage.test.tsx
index bb18d421ccf..4171dda0abe 100644
--- a/packages/cli/src/ui/components/messages/ToolConfirmationMessage.test.tsx
+++ b/packages/cli/src/ui/components/messages/ToolConfirmationMessage.test.tsx
@@ -282,6 +282,29 @@ describe('ToolConfirmationMessage', () => {
       expect(frame).not.toContain('Always allow for this user');
     });
 
+    it('renders exec security warnings', () => {
+      const confirmationDetails: ToolCallConfirmationDetails = {
+        type: 'exec',
+        title: 'Confirm Execution',
+        command: 'python3 -c "print($(echo hello))"',
+        rootCommand: 'python3',
+        securityWarnings: ['Contains command_substitution'],
+        onConfirm: vi.fn(),
+      };
+
+      const { lastFrame } = renderWithProviders(
+        <ToolConfirmationMessage
+          confirmationDetails={confirmationDetails}
+          config={mockConfig}
+          availableTerminalHeight={30}
+          contentWidth={80}
+          compactMode={true}
+        />,
+      );
+
+      expect(lastFrame()).toContain('Contains command_substitution');
+    });
+
     it('renders MCP server and tool name for mcp confirmations', () => {
       const confirmationDetails: ToolCallConfirmationDetails = {
         type: 'mcp',
diff --git a/packages/cli/src/ui/components/messages/ToolConfirmationMessage.tsx b/packages/cli/src/ui/components/messages/ToolConfirmationMessage.tsx
index 07b66b2dd25..dfff8fb2549 100644
--- a/packages/cli/src/ui/components/messages/ToolConfirmationMessage.tsx
+++ b/packages/cli/src/ui/components/messages/ToolConfirmationMessage.tsx
@@ -273,6 +273,11 @@ export const ToolConfirmationMessage: React.FC<
             </Box>
           </MaxSizedBox>
         </Box>
+        {executionProps.securityWarnings?.map((warning) => (
+          <Box key={warning} paddingX={1} marginLeft={1} marginTop={1}>
+            <Text color={theme.status.warning}>{warning}</Text>
+          </Box>
+        ))}
       </Box>
     );
   } else if (confirmationDetails.type === 'plan') {
diff --git a/packages/core/src/confirmation-bus/types.ts b/packages/core/src/confirmation-bus/types.ts
index e44fb8d940f..fe0bb0d51ce 100644
--- a/packages/core/src/confirmation-bus/types.ts
+++ b/packages/core/src/confirmation-bus/types.ts
@@ -78,6 +78,7 @@ export type SerializableConfirmationDetails =
       rootCommand: string;
       rootCommands: string[];
       commands?: string[];
+      securityWarnings?: string[];
     }
   | {
       type: 'mcp';
diff --git a/packages/core/src/permissions/permission-manager.test.ts b/packages/core/src/permissions/permission-manager.test.ts
index 32d529d5a24..d399035525c 100644
--- a/packages/core/src/permissions/permission-manager.test.ts
+++ b/packages/core/src/permissions/permission-manager.test.ts
@@ -1256,6 +1256,22 @@ describe('PermissionManager', () => {
       ).toBe('ask');
     });
 
+    it('one sub-command has command substitution → ask with user confirmation', async () => {
+      pm = new PermissionManager(
+        makeConfig({
+          permissionsAllow: ['Bash(echo *)'],
+        }),
+      );
+      pm.initialize();
+
+      expect(
+        await pm.evaluate({
+          toolName: 'run_shell_command',
+          command: 'echo hello && python3 -c "print($(echo hello))"',
+        }),
+      ).toBe('ask');
+    });
+
     it('one sub-command denied → deny', async () => {
       pm = new PermissionManager(
         makeConfig({
diff --git a/packages/core/src/permissions/permission-manager.ts b/packages/core/src/permissions/permission-manager.ts
index 20bd0f4d278..be5c464b182 100644
--- a/packages/core/src/permissions/permission-manager.ts
+++ b/packages/core/src/permissions/permission-manager.ts
@@ -348,7 +348,7 @@ export class PermissionManager {
    *
    * When a sub-command returns 'default' (no rule matches), it is resolved to
    * the actual default permission using AST analysis:
-   *   - Command substitution detected → 'deny'
+   *   - Command substitution detected → 'ask'
    *   - Read-only command (cd, ls, git status, etc.) → 'allow'
    *   - Otherwise → 'ask'
    *
@@ -403,14 +403,14 @@ export class PermissionManager {
    * This mirrors the logic in ShellToolInvocation.getDefaultPermission().
    *
    * @param command - The shell command to analyze.
-   * @returns 'deny' for command substitution, 'allow' for read-only, 'ask' otherwise.
+   * @returns 'ask' for command substitution, 'allow' for read-only, 'ask' otherwise.
    */
   private async resolveDefaultPermission(
     command: string,
   ): Promise<'allow' | 'ask' | 'deny'> {
-    // Security: command substitution ($(), ``, <(), >()) → deny
+    // Security: command substitution ($(), ``, <(), >()) needs explicit user confirmation.
     if (detectCommandSubstitution(command)) {
-      return 'deny';
+      return 'ask';
     }
 
     // AST-based read-only detection
diff --git a/packages/core/src/tools/shell.test.ts b/packages/core/src/tools/shell.test.ts
index 706b16fdb10..4ac0b099c36 100644
--- a/packages/core/src/tools/shell.test.ts
+++ b/packages/core/src/tools/shell.test.ts
@@ -4873,6 +4873,22 @@ describe('ShellTool', () => {
       expect(details.type).toBe('exec');
     });
 
+    it('should warn when a shell confirmation contains command substitution', async () => {
+      const invocation = shellTool.build({
+        command: 'python3 -c "print($(echo hello))"',
+        is_background: false,
+      });
+
+      const details = await invocation.getConfirmationDetails(
+        new AbortController().signal,
+      );
+
+      expect(details).toMatchObject({
+        type: 'exec',
+        securityWarnings: ['Contains command_substitution'],
+      });
+    });
+
     it('should exclude read-only sub-commands from confirmation details in compound commands', async () => {
       // "cd" is read-only, "npm run build" is not
       const params = {
diff --git a/packages/core/src/tools/shell.ts b/packages/core/src/tools/shell.ts
index 095c2a4b41e..3150f2233c1 100644
--- a/packages/core/src/tools/shell.ts
+++ b/packages/core/src/tools/shell.ts
@@ -47,6 +47,7 @@ import {
   getCommandRoot,
   getCommandRoots,
   getShellConfiguration,
+  detectCommandSubstitution,
   type ShellConfiguration,
   type ShellType,
   splitCommands,
@@ -1464,12 +1465,17 @@ export class ShellToolInvocation extends BaseToolInvocation<
       debugLogger.warn('Failed to extract command rules:', e);
     }
 
+    const securityWarnings = detectCommandSubstitution(command)
+      ? ['Contains command_substitution']
+      : undefined;
+
     const confirmationDetails: ToolExecuteConfirmationDetails = {
       type: 'exec',
       title: 'Confirm Shell Command',
       command: this.params.command,
       rootCommand: rootCommands.join(', '),
       permissionRules,
+      securityWarnings,
       onConfirm: async (
         _outcome: ToolConfirmationOutcome,
         _payload?: ToolConfirmationPayload,
diff --git a/packages/core/src/tools/tools.ts b/packages/core/src/tools/tools.ts
index 827eb2a86b5..6991ea2d40d 100644
--- a/packages/core/src/tools/tools.ts
+++ b/packages/core/src/tools/tools.ts
@@ -44,7 +44,7 @@ export interface ToolInvocation<
    *
    * - `'allow'` — inherently safe (e.g., read-only commands, `cat`, `ls`).
    * - `'ask'`   — may have side effects, needs user or PM confirmation.
-   * - `'deny'`  — security violation (e.g., command substitution in shell).
+   * - `'deny'`  — explicit security or policy violation.
    *
    * The coreToolScheduler uses this as the *default* permission which may be
    * overridden by PermissionManager rules at L4.
@@ -692,6 +692,8 @@ export interface ToolExecuteConfirmationDetails {
   rootCommand: string;
   /** Permission rules extracted by extractCommandRules(), used for display and persistence. */
   permissionRules?: string[];
+  /** Warnings surfaced to the confirmation UI before the user approves execution. */
+  securityWarnings?: string[];
 }
 
 export interface ToolMcpConfirmationDetails {