diff --git a/packages/cli/src/setup-agents.test.ts b/packages/cli/src/setup-agents.test.ts
index ee5c7718..38b968a6 100644
--- a/packages/cli/src/setup-agents.test.ts
+++ b/packages/cli/src/setup-agents.test.ts
@@ -86,6 +86,9 @@ describe('setup agents', () => {
     expect(skill).toContain('must not print secrets');
     expect(skill).toContain('status --json');
     expect(skill).toContain('sl list --json');
+    expect(skill).toContain('sl query');
+    expect(skill).toContain('--format json');
+    expect(skill).not.toContain('sl query --json');
     expect(skill).not.toContain('agent ');
     expect(skill).not.toContain('sql execute');
     expect(await readKtxAgentInstallManifest(tempDir)).toMatchObject({
@@ -120,6 +123,8 @@ describe('setup agents', () => {
     expect(skill).not.toContain('`ktx agent');
     expect(skill).toContain('status --json');
     expect(skill).toContain('sl query');
+    expect(skill).toContain('--format json');
+    expect(skill).not.toContain('sl query --json');
     expect(skill).not.toContain('sql execute');
   });
 
diff --git a/packages/cli/src/setup-agents.ts b/packages/cli/src/setup-agents.ts
index 7a18a969..a6dfa47f 100644
--- a/packages/cli/src/setup-agents.ts
+++ b/packages/cli/src/setup-agents.ts
@@ -121,7 +121,8 @@ function ktxCommandLine(launcher: KtxCliLauncher, args: string[]): string {
 }
 
 function cliInstructionContent(input: { projectDir: string; launcher: KtxCliLauncher }): string {
-  const projectDirArgs = ['--json', '--project-dir', input.projectDir];
+  const projectDirArgs = ['--project-dir', input.projectDir];
+  const jsonProjectDirArgs = ['--json', ...projectDirArgs];
   return [
     '---',
     'name: ktx',
@@ -138,9 +139,9 @@ function cliInstructionContent(input: { projectDir: string; launcher: KtxCliLaun
     '',
     'Available commands:',
     '',
-    `- \`${ktxCommandLine(input.launcher, ['status', ...projectDirArgs])}\``,
-    `- \`${ktxCommandLine(input.launcher, ['sl', 'list', ...projectDirArgs])}\``,
-    `- \`${ktxCommandLine(input.launcher, ['sl', 'search', '<text>', ...projectDirArgs, '--connection-id', '<id>'])}\``,
+    `- \`${ktxCommandLine(input.launcher, ['status', ...jsonProjectDirArgs])}\``,
+    `- \`${ktxCommandLine(input.launcher, ['sl', 'list', ...jsonProjectDirArgs])}\``,
+    `- \`${ktxCommandLine(input.launcher, ['sl', 'search', '<text>', ...jsonProjectDirArgs, '--connection-id', '<id>'])}\``,
     `- \`${ktxCommandLine(input.launcher, [
       'sl',
       'query',
@@ -149,11 +150,13 @@ function cliInstructionContent(input: { projectDir: string; launcher: KtxCliLaun
       '<id>',
       '--query-file',
       '<path>',
+      '--format',
+      'json',
       '--execute',
       '--max-rows',
       '100',
     ])}\``,
-    `- \`${ktxCommandLine(input.launcher, ['wiki', 'search', '<query>', ...projectDirArgs, '--limit', '10'])}\``,
+    `- \`${ktxCommandLine(input.launcher, ['wiki', 'search', '<query>', ...jsonProjectDirArgs, '--limit', '10'])}\``,
     '',
     'Use semantic-layer queries before direct database access. Do not print secrets or credential references.',
     '',