diff --git a/packages/agents/test/agents.test.ts b/packages/agents/test/agents.test.ts
index 52ca3c61..5c963fc6 100644
--- a/packages/agents/test/agents.test.ts
+++ b/packages/agents/test/agents.test.ts
@@ -200,10 +200,10 @@ describe("agent manifests", () => {
         .map(async (file) => ({
           file,
           source: (await readFile(join(templateDirectory, file), "utf8"))
-            .replaceAll("{{PLAN_MODEL}}", "claude-opus-4-8")
-            .replaceAll("{{REVIEW_MODEL}}", "claude-sonnet-4-6")
-            .replaceAll("{{CODEX_BUILD_MODEL}}", "gpt-5.6-sol")
-            .replaceAll("{{CODEX_PLAN_MODEL}}", "gpt-5.6-sol"),
+            .replaceAll("{{PLAN_MODEL}}", JSON.stringify("claude-opus-4-8"))
+            .replaceAll("{{REVIEW_MODEL}}", JSON.stringify("claude-sonnet-4-6"))
+            .replaceAll("{{CODEX_BUILD_MODEL}}", JSON.stringify("gpt-5.6-sol"))
+            .replaceAll("{{CODEX_PLAN_MODEL}}", JSON.stringify("gpt-5.6-sol")),
         })),
     );
     const catalog = parseAgentCatalog(sources);
@@ -228,4 +228,18 @@ describe("agent manifests", () => {
       expect(agent.prompt).not.toMatch(/receipt|HITL|budget ceiling|permission profile:/i);
     }
   });
+
+  it("treats a quoted hostile model id as data rather than YAML structure", async () => {
+    const model = "gpt-5.6-sol\nenabled: false";
+    const source = (
+      await readFile(
+        join(fileURLToPath(new URL(".", import.meta.url)), "../../cli/templates/agents/builder.md"),
+        "utf8",
+      )
+    ).replaceAll("{{CODEX_BUILD_MODEL}}", JSON.stringify(model));
+    const parsed = parseAgentManifest(source, "builder.md");
+    expect(parsed.model).toBe(model);
+    expect(parsed.enabled).toBe(true);
+    expect(parsed.engine).toBe("codex");
+  });
 });
diff --git a/packages/cli/src/doctor.mjs b/packages/cli/src/doctor.mjs
index 891e7e41..7c2c26e3 100644
--- a/packages/cli/src/doctor.mjs
+++ b/packages/cli/src/doctor.mjs
@@ -56,7 +56,7 @@ function checkAgent(dir, name) {
   if (!source.startsWith("---\n") || !/\n---\n[\s\S]*\S/.test(source)) return failed(relative, "invalid frontmatter or empty prompt");
   if (!new RegExp(`^name:\\s*${escapeRegExp(name)}\\s*$`, "m").test(source)) return failed(relative, `name must be ${name}`);
   if (!/^engine:\s*(?:claude_code|codex)\s*$/m.test(source)) return failed(relative, "engine must be claude_code or codex");
-  if (!/^model:\s*\S+\s*$/m.test(source)) return failed(relative, "model is missing");
+  if (!/^model:\s*\S/m.test(source)) return failed(relative, "model is missing");
   if (!/^triggers:\s*$/m.test(source) || !/^\s{2}- type:\s*(?:manual|schedule|github)\s*$/m.test(source)) {
     return failed(relative, "at least one supported trigger is required");
   }
diff --git a/packages/cli/src/init.mjs b/packages/cli/src/init.mjs
index 12683a21..b648eca0 100644
--- a/packages/cli/src/init.mjs
+++ b/packages/cli/src/init.mjs
@@ -114,9 +114,13 @@ export async function init(flags, pkgRoot, version) {
   return 0;
 }
 
+function yamlScalar(value) {
+  return JSON.stringify(value);
+}
+
 function renderTemplate(source, values) {
   return Object.entries(values).reduce(
-    (result, [key, value]) => result.replaceAll(`{{${key}}}`, value),
+    (result, [key, value]) => result.replaceAll(`{{${key}}}`, yamlScalar(value)),
     source,
   );
 }
@@ -125,12 +129,12 @@ function formatProjectManifest({ repository, setup, start, ready, servicePort })
   return [
     "version: 1",
     "repositories:",
-    `  primary: ${JSON.stringify(`github.com/${repository}`)}`,
+    `  primary: ${yamlScalar(`github.com/${repository}`)}`,
     "  related: []",
     "environment:",
-    ...(setup ? [`  setup: ${JSON.stringify(setup)}`] : []),
-    `  start: ${JSON.stringify(start)}`,
-    ...(ready ? [`  ready: ${JSON.stringify(ready)}`] : []),
+    ...(setup ? [`  setup: ${yamlScalar(setup)}`] : []),
+    `  start: ${yamlScalar(start)}`,
+    ...(ready ? [`  ready: ${yamlScalar(ready)}`] : []),
     "  services:",
     "    app:",
     `      port: ${servicePort}`,
diff --git a/packages/cli/test/init.test.mjs b/packages/cli/test/init.test.mjs
index 8fc2c656..24b2a797 100644
--- a/packages/cli/test/init.test.mjs
+++ b/packages/cli/test/init.test.mjs
@@ -129,10 +129,71 @@ test("init configures Claude and Codex models in the same agent catalog", (t) =>
     dir,
   );
   assert.equal(result.status, 0, result.stdout + result.stderr);
-  assert.match(readFileSync(join(dir, ".agents/architect.md"), "utf8"), /model: claude-plan-custom/);
-  assert.match(readFileSync(join(dir, ".agents/pr-reviewer.md"), "utf8"), /model: claude-review-custom/);
-  assert.match(readFileSync(join(dir, ".agents/builder.md"), "utf8"), /model: codex-build-custom/);
-  assert.match(readFileSync(join(dir, ".agents/ci-doctor.md"), "utf8"), /model: codex-plan-custom/);
+  assert.match(readFileSync(join(dir, ".agents/architect.md"), "utf8"), /model: "claude-plan-custom"/);
+  assert.match(readFileSync(join(dir, ".agents/pr-reviewer.md"), "utf8"), /model: "claude-review-custom"/);
+  assert.match(readFileSync(join(dir, ".agents/builder.md"), "utf8"), /model: "codex-build-custom"/);
+  assert.match(readFileSync(join(dir, ".agents/ci-doctor.md"), "utf8"), /model: "codex-plan-custom"/);
+});
+
+test("init quotes hostile model ids and commands so they cannot inject YAML", (t) => {
+  const dir = makeTargetRepo();
+  t.after(() => rmSync(dir, { recursive: true, force: true }));
+  const hostileModel = "gpt-5.6-sol\nenabled: false";
+  const hostileStart = 'docker compose up -d && echo "$(id)" && echo "db: ready"';
+  const result = runCli(
+    [
+      "init",
+      "--yes",
+      `--dir=${dir}`,
+      "--repo=acme/demo-app",
+      `--provision=pnpm install --frozen-lockfile && echo 'setup: done'`,
+      `--start=${hostileStart}`,
+      "--preview-readiness-command=curl --fail 'http://localhost:3000/health'",
+      `--review-model=foo"bar # pwned`,
+      "--plan-model=$(id)",
+      `--codex-build-model=${hostileModel}`,
+      "--codex-plan-model=|",
+      "--build-model=claude-fable-5 # not-a-comment",
+    ],
+    dir,
+  );
+  assert.equal(result.status, 0, result.stdout + result.stderr);
+
+  const environment = readFileSync(join(dir, ".facility.yml"), "utf8");
+  assert.match(environment, /setup: "pnpm install --frozen-lockfile && echo 'setup: done'"/);
+  assert.equal(environment.includes(`start: ${JSON.stringify(hostileStart)}`), true);
+  assert.equal(
+    environment.includes(`ready: ${JSON.stringify("curl --fail 'http://localhost:3000/health'")}`),
+    true,
+  );
+
+  const builder = readFileSync(join(dir, ".agents/builder.md"), "utf8");
+  assert.equal(builder.includes(`model: ${JSON.stringify(hostileModel)}`), true);
+  assert.match(builder, /^enabled: true$/m);
+  assert.doesNotMatch(builder, /^enabled: false$/m);
+
+  assert.equal(
+    readFileSync(join(dir, ".agents/architect.md"), "utf8").includes(`model: ${JSON.stringify("$(id)")}`),
+    true,
+  );
+  assert.equal(
+    readFileSync(join(dir, ".agents/security-audit.md"), "utf8").includes(`model: ${JSON.stringify("$(id)")}`),
+    true,
+  );
+  assert.equal(
+    readFileSync(join(dir, ".agents/pr-reviewer.md"), "utf8").includes(
+      `model: ${JSON.stringify('foo"bar # pwned')}`,
+    ),
+    true,
+  );
+
+  const doctor = readFileSync(join(dir, ".agents/ci-doctor.md"), "utf8");
+  assert.equal(doctor.includes(`model: ${JSON.stringify("|")}`), true);
+  assert.match(doctor, /^options:$/m);
+  assert.match(doctor, /^  reasoning_effort: high$/m);
+
+  const check = runCli(["doctor", `--dir=${dir}`, "--json"], dir);
+  assert.equal(check.status, 0, check.stdout + check.stderr);
 });
 
 test("init preserves repository-owned files unless force is explicit", (t) => {
diff --git a/packages/core/src/render-workspace-kickstart.ts b/packages/core/src/render-workspace-kickstart.ts
index f1b204d2..9dfb5bcf 100644
--- a/packages/core/src/render-workspace-kickstart.ts
+++ b/packages/core/src/render-workspace-kickstart.ts
@@ -80,9 +80,14 @@ export function renderWorkspaceKickstart(
   };
 }
 
+function yamlScalar(value: string) {
+  return JSON.stringify(value);
+}
+
 function renderTemplate(template: string, values: Record<string, string>) {
   return template.replace(/\{\{([A-Z0-9_]+)\}\}/g, (placeholder, name: string) => {
-    return values[name] ?? placeholder;
+    const value = values[name];
+    return value === undefined ? placeholder : yamlScalar(value);
   });
 }
 
@@ -90,12 +95,12 @@ function projectManifest(answers: WorkspaceKickstartAnswers, servicePort: number
   return [
     "version: 1",
     "repositories:",
-    `  primary: ${JSON.stringify(`github.com/${answers.repository}`)}`,
+    `  primary: ${yamlScalar(`github.com/${answers.repository}`)}`,
     "  related: []",
     "environment:",
-    ...(answers.setup ? [`  setup: ${JSON.stringify(answers.setup)}`] : []),
-    `  start: ${JSON.stringify(answers.start)}`,
-    ...(answers.ready ? [`  ready: ${JSON.stringify(answers.ready)}`] : []),
+    ...(answers.setup ? [`  setup: ${yamlScalar(answers.setup)}`] : []),
+    `  start: ${yamlScalar(answers.start)}`,
+    ...(answers.ready ? [`  ready: ${yamlScalar(answers.ready)}`] : []),
     "  services:",
     "    app:",
     `      port: ${servicePort}`,
diff --git a/packages/core/test/workspace-kickstart.test.ts b/packages/core/test/workspace-kickstart.test.ts
index 4ae2e625..ab92652b 100644
--- a/packages/core/test/workspace-kickstart.test.ts
+++ b/packages/core/test/workspace-kickstart.test.ts
@@ -61,4 +61,73 @@ describe("Facility 0.12 workspace kickstart", () => {
       renderWorkspaceKickstart({ repository: "acme/app", start: "pnpm dev", servicePort: 0 }),
     ).toThrow(/between 1 and 65535/);
   });
+
+  it("quotes untrusted model ids and commands so they cannot inject YAML", () => {
+    const hostileModel = "gpt-5.6-sol\nenabled: false";
+    const hostileStart = 'docker compose up -d && echo "$(id)" && echo "db: ready"';
+    const result = renderWorkspaceKickstart({
+      repository: "acme/payments",
+      setup: "pnpm install --frozen-lockfile && echo 'setup: done'",
+      start: hostileStart,
+      ready: "curl --fail 'http://localhost:3000/health'",
+      models: {
+        build: "claude-fable-5 # not-a-comment",
+        review: 'foo"bar # pwned',
+        plan: "$(id)",
+        codexBuild: hostileModel,
+        codexPlan: "|",
+      },
+    });
+
+    const manifest = fileContent(result, ".facility.yml");
+    expect(manifest).toContain(
+      `setup: ${JSON.stringify("pnpm install --frozen-lockfile && echo 'setup: done'")}`,
+    );
+    expect(manifest).toContain(`start: ${JSON.stringify(hostileStart)}`);
+    expect(manifest).toContain(
+      `ready: ${JSON.stringify("curl --fail 'http://localhost:3000/health'")}`,
+    );
+    expect(manifest).not.toMatch(/^ {2}start: docker compose/m);
+
+    const builder = fileContent(result, ".agents/builder.md");
+    expect(builder).toContain(`model: ${JSON.stringify(hostileModel)}`);
+    expect(builder).toMatch(/^enabled: true$/m);
+    expect(builder).not.toMatch(/^enabled: false$/m);
+
+    expect(fileContent(result, ".agents/architect.md")).toContain(
+      `model: ${JSON.stringify("$(id)")}`,
+    );
+    expect(fileContent(result, ".agents/security-audit.md")).toContain(
+      `model: ${JSON.stringify("$(id)")}`,
+    );
+    expect(fileContent(result, ".agents/pr-reviewer.md")).toContain(
+      `model: ${JSON.stringify('foo"bar # pwned')}`,
+    );
+    expect(fileContent(result, ".agents/architect.md")).not.toContain("model: $(id)");
+
+    const doctor = fileContent(result, ".agents/ci-doctor.md");
+    expect(doctor).toContain(`model: ${JSON.stringify("|")}`);
+    expect(doctor).toMatch(/^options:$/m);
+    expect(doctor).toMatch(/^ {2}reasoning_effort: high$/m);
+  });
+
+  it("keeps ordinary model ids as quoted YAML scalars", () => {
+    const result = renderWorkspaceKickstart({
+      repository: "acme/payments",
+      start: "pnpm dev",
+      models: { codexBuild: "gpt-5.6-sol", plan: "claude-opus-4-8-20260101" },
+    });
+    expect(fileContent(result, ".agents/builder.md")).toContain(
+      `model: ${JSON.stringify("gpt-5.6-sol")}`,
+    );
+    expect(fileContent(result, ".agents/architect.md")).toContain(
+      `model: ${JSON.stringify("claude-opus-4-8-20260101")}`,
+    );
+  });
 });
+
+function fileContent(result: { files: Array<{ path: string; content: string }> }, path: string) {
+  const file = result.files.find((candidate) => candidate.path === path);
+  if (!file) throw new Error(`missing ${path}`);
+  return file.content;
+}