diff --git a/get-shit-done/bin/lib/config.cjs b/get-shit-done/bin/lib/config.cjs
index 5f1ae3d38..fd1f11ae9 100644
--- a/get-shit-done/bin/lib/config.cjs
+++ b/get-shit-done/bin/lib/config.cjs
@@ -28,6 +28,7 @@ const VALID_CONFIG_KEYS = new Set([
   'workflow.subagent_timeout',
   'hooks.context_warnings',
   'project_code', 'phase_naming',
+  'manager.flags.discuss', 'manager.flags.plan', 'manager.flags.execute',
 ]);
 
 /**
diff --git a/get-shit-done/bin/lib/core.cjs b/get-shit-done/bin/lib/core.cjs
index 81b8cd9b4..ed316146d 100644
--- a/get-shit-done/bin/lib/core.cjs
+++ b/get-shit-done/bin/lib/core.cjs
@@ -314,6 +314,7 @@ function loadConfig(cwd) {
       subagent_timeout: get('subagent_timeout', { section: 'workflow', field: 'subagent_timeout' }) ?? defaults.subagent_timeout,
       model_overrides: parsed.model_overrides || null,
       agent_skills: parsed.agent_skills || {},
+      manager: parsed.manager || {},
     };
   } catch {
     return defaults;
diff --git a/get-shit-done/bin/lib/init.cjs b/get-shit-done/bin/lib/init.cjs
index dd126eb42..dc0f8e03c 100644
--- a/get-shit-done/bin/lib/init.cjs
+++ b/get-shit-done/bin/lib/init.cjs
@@ -1026,6 +1026,14 @@ function cmdInitManager(cwd, raw) {
   });
 
   const completedCount = phases.filter(p => p.disk_status === 'complete').length;
+
+  // Read manager flags from config (passthrough flags for each step)
+  const managerFlags = {
+    discuss: (config.manager && config.manager.flags && config.manager.flags.discuss) || '',
+    plan: (config.manager && config.manager.flags && config.manager.flags.plan) || '',
+    execute: (config.manager && config.manager.flags && config.manager.flags.execute) || '',
+  };
+
   const result = {
     milestone_version: milestone.version,
     milestone_name: milestone.name,
@@ -1039,6 +1047,7 @@ function cmdInitManager(cwd, raw) {
     project_exists: pathExistsInternal(cwd, '.planning/PROJECT.md'),
     roadmap_exists: true,
     state_exists: true,
+    manager_flags: managerFlags,
   };
 
   output(withProjectRoot(cwd, result), raw);
diff --git a/get-shit-done/references/planning-config.md b/get-shit-done/references/planning-config.md
index e598f6214..aba562b98 100644
--- a/get-shit-done/references/planning-config.md
+++ b/get-shit-done/references/planning-config.md
@@ -14,6 +14,13 @@ Configuration options for `.planning/` directory behavior.
   "phase_branch_template": "gsd/phase-{phase}-{slug}",
   "milestone_branch_template": "gsd/{milestone}-{slug}",
   "quick_branch_template": null
+},
+"manager": {
+  "flags": {
+    "discuss": "",
+    "plan": "",
+    "execute": ""
+  }
 }
 ```
 
@@ -28,6 +35,9 @@ Configuration options for `.planning/` directory behavior.
 | `git.quick_branch_template` | `null` | Optional branch template for quick-task runs |
 | `workflow.use_worktrees` | `true` | Whether executor agents run in isolated git worktrees. Set to `false` to disable worktrees — agents execute sequentially on the main working tree instead. Recommended for solo developers or when worktree merges cause issues. |
 | `workflow.subagent_timeout` | `300000` | Timeout in milliseconds for parallel subagent tasks (e.g. codebase mapping). Increase for large codebases or slower models. Default: 300000 (5 minutes). |
+| `manager.flags.discuss` | `""` | Flags passed to `/gsd:discuss-phase` when dispatched from manager (e.g. `"--auto --analyze"`) |
+| `manager.flags.plan` | `""` | Flags passed to plan workflow when dispatched from manager |
+| `manager.flags.execute` | `""` | Flags passed to execute workflow when dispatched from manager |
 </config_schema>
 
 <commit_docs_behavior>
diff --git a/get-shit-done/workflows/manager.md b/get-shit-done/workflows/manager.md
index 4eba9624b..fc3c64ee0 100644
--- a/get-shit-done/workflows/manager.md
+++ b/get-shit-done/workflows/manager.md
@@ -23,7 +23,14 @@ INIT=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" init manager)
 if [[ "$INIT" == @file:* ]]; then INIT=$(cat "${INIT#@file:}"); fi
 ```
 
-Parse JSON for: `milestone_version`, `milestone_name`, `phase_count`, `completed_count`, `in_progress_count`, `phases`, `recommended_actions`, `all_complete`, `waiting_signal`.
+Parse JSON for: `milestone_version`, `milestone_name`, `phase_count`, `completed_count`, `in_progress_count`, `phases`, `recommended_actions`, `all_complete`, `waiting_signal`, `manager_flags`.
+
+`manager_flags` contains per-step passthrough flags from config:
+- `manager_flags.discuss` — appended to `/gsd:discuss-phase` args (e.g. `"--auto --analyze"`)
+- `manager_flags.plan` — appended to plan agent init command
+- `manager_flags.execute` — appended to execute agent init command
+
+These are empty strings by default. Set via: `gsd-tools config-set manager.flags.discuss "--auto --analyze"`
 
 **If error:** Display the error message and exit.
 
@@ -193,24 +200,24 @@ When the user selects a compound option:
 2. **Then run the inline discuss:**
 
 ```
-Skill(skill="gsd:discuss-phase", args="{PHASE_NUM}")
+Skill(skill="gsd:discuss-phase", args="{PHASE_NUM} {manager_flags.discuss}")
 ```
 
 After discuss completes, loop back to dashboard step (background agents continue running).
 
 ### Discuss Phase N
 
-Discussion is interactive — needs user input. Run inline:
+Discussion is interactive — needs user input. Run inline with any configured flags:
 
 ```
-Skill(skill="gsd:discuss-phase", args="{PHASE_NUM}")
+Skill(skill="gsd:discuss-phase", args="{PHASE_NUM} {manager_flags.discuss}")
 ```
 
 After discuss completes, loop back to dashboard step.
 
 ### Plan Phase N
 
-Planning runs autonomously. Spawn a background agent that delegates to the Skill pipeline:
+Planning runs autonomously. Spawn a background agent that delegates to the Skill pipeline with any configured flags:
 
 ```
 Task(
@@ -221,9 +228,10 @@ Task(
 Working directory: {cwd}
 Phase: {N} — {phase_name}
 Goal: {goal}
+Manager flags: {manager_flags.plan}
 
-Run the plan-phase Skill:
-Skill(skill=\"gsd:plan-phase\", args=\"{N} --auto\")
+Run the plan-phase Skill with any configured manager flags:
+Skill(skill=\"gsd:plan-phase\", args=\"{N} --auto {manager_flags.plan}\")
 
 This delegates to the full plan-phase pipeline including local patches, research, plan-checker, and all quality gates.
 
@@ -241,7 +249,7 @@ Loop back to dashboard step.
 
 ### Execute Phase N
 
-Execution runs autonomously. Spawn a background agent that delegates to the Skill pipeline:
+Execution runs autonomously. Spawn a background agent that delegates to the Skill pipeline with any configured flags:
 
 ```
 Task(
@@ -252,9 +260,10 @@ Task(
 Working directory: {cwd}
 Phase: {N} — {phase_name}
 Goal: {goal}
+Manager flags: {manager_flags.execute}
 
-Run the execute-phase Skill:
-Skill(skill=\"gsd:execute-phase\", args=\"{N}\")
+Run the execute-phase Skill with any configured manager flags:
+Skill(skill=\"gsd:execute-phase\", args=\"{N} {manager_flags.execute}\")
 
 This delegates to the full execute-phase pipeline including local patches, branching, wave-based execution, verification, and all quality gates.
 
diff --git a/tests/init-manager.test.cjs b/tests/init-manager.test.cjs
index c133093bd..08d685ddb 100644
--- a/tests/init-manager.test.cjs
+++ b/tests/init-manager.test.cjs
@@ -413,4 +413,44 @@ describe('init manager', () => {
     // macOS resolves /var → /private/var; normalize both sides
     assert.strictEqual(fs.realpathSync(output.project_root), fs.realpathSync(tmpDir));
   });
+
+  test('output includes manager_flags defaults when not configured', () => {
+    writeState(tmpDir);
+    writeRoadmap(tmpDir, [{ number: '1', name: 'Test' }]);
+
+    const result = runGsdTools('init manager', tmpDir);
+    const output = JSON.parse(result.output);
+
+    assert.ok(output.manager_flags, 'should include manager_flags');
+    assert.strictEqual(output.manager_flags.discuss, '');
+    assert.strictEqual(output.manager_flags.plan, '');
+    assert.strictEqual(output.manager_flags.execute, '');
+  });
+
+  test('output includes manager_flags from config when set', () => {
+    writeState(tmpDir);
+    writeRoadmap(tmpDir, [{ number: '1', name: 'Test' }]);
+
+    // Write config with manager flags
+    fs.writeFileSync(
+      path.join(tmpDir, '.planning', 'config.json'),
+      JSON.stringify({
+        manager: {
+          flags: {
+            discuss: '--auto --analyze',
+            plan: '--skip-research',
+            execute: '--interactive',
+          }
+        }
+      })
+    );
+
+    const result = runGsdTools('init manager', tmpDir);
+    const output = JSON.parse(result.output);
+
+    assert.ok(output.manager_flags, 'should include manager_flags');
+    assert.strictEqual(output.manager_flags.discuss, '--auto --analyze');
+    assert.strictEqual(output.manager_flags.plan, '--skip-research');
+    assert.strictEqual(output.manager_flags.execute, '--interactive');
+  });
 });