diff --git a/CHANGELOG.md b/CHANGELOG.md
index e16f9edf..7f709b8d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+### Fixed
+
+- **Settings preservation during evolve**: `jumbo evolve --yes` now additively inserts missing `.jumbo/settings.jsonc` defaults without overwriting customized known values or unknown user settings, and invalid JSONC settings files fail clearly instead of being partially rewritten.
+
 ## [3.12.0] - 2026-07-04
 
 ### Added
diff --git a/docs/getting-started/what-jumbo-creates.md b/docs/getting-started/what-jumbo-creates.md
index 145a977a..506535df 100644
--- a/docs/getting-started/what-jumbo-creates.md
+++ b/docs/getting-started/what-jumbo-creates.md
@@ -106,6 +106,7 @@ The `.jumbo/` directory is **local project memory**. It is not yet designed for
 ## Configuration
 
 Jumbo stores project-level settings in `.jumbo/settings.jsonc`. The file supports comments (JSONC format).
+When `jumbo evolve --yes` or settings persistence updates this file, Jumbo preserves explicit values and unknown entries while adding any missing defaults.
 
 Default contents:
 
diff --git a/docs/reference/commands/maintenance.md b/docs/reference/commands/maintenance.md
index b927bbc0..286bf74d 100644
--- a/docs/reference/commands/maintenance.md
+++ b/docs/reference/commands/maintenance.md
@@ -72,11 +72,11 @@ Runs the complete installation update workflow in sequence:
 3. Convert legacy component-coupling dependencies into relations
 4. Refresh `AGENTS.md` and managed agent instruction files
 5. Sync Jumbo-managed skills from `assets/skills/`
-6. Ensure settings files exist
+6. Ensure settings files exist and add missing default settings without overwriting user values
 7. Refresh managed harness and hook configuration
 8. Rebuild database projections from the event store
 
-The command is designed to be idempotent. Re-running it after a successful evolve should not create duplicate events or duplicate relations.
+The command is designed to be idempotent. Re-running it after a successful evolve should not create duplicate events or duplicate relations. Existing `.jumbo/settings.jsonc` files are upgraded additively: missing defaults are inserted, explicit values and unknown entries are preserved, and invalid JSONC fails instead of being partially rewritten.
 
 ### Examples
 
diff --git a/src/infrastructure/settings/FsSettingsInitializer.ts b/src/infrastructure/settings/FsSettingsInitializer.ts
index 9c589a34..3fd03fb1 100644
--- a/src/infrastructure/settings/FsSettingsInitializer.ts
+++ b/src/infrastructure/settings/FsSettingsInitializer.ts
@@ -2,12 +2,15 @@ import fs from "fs-extra";
 import path from "path";
 import { ISettingsInitializer } from "../../application/settings/ISettingsInitializer.js";
 import { PlannedFileChange } from "../../application/context/project/init/PlannedFileChange.js";
+import { DEFAULT_SETTINGS } from "./DefaultSettings.js";
+import { JsonObject, applyMissingDefaults, assertValidJsonc } from "./JsoncSettingsEditor.js";
 
 /**
- * FsSettingsInitializer - Creates settings file with defaults if it doesn't exist.
+ * FsSettingsInitializer - Creates settings file with defaults if it doesn't exist,
+ * and additively fills in any missing default sections or fields if it does.
  *
- * Called during bootstrap to ensure settings infrastructure is ready.
- * Only creates the file if missing - doesn't overwrite existing settings.
+ * Called during bootstrap and evolve to ensure settings infrastructure is current.
+ * Existing explicit values and unknown entries are always preserved.
  */
 export class FsSettingsInitializer implements ISettingsInitializer {
   private readonly settingsFilePath: string;
@@ -17,8 +20,8 @@ export class FsSettingsInitializer implements ISettingsInitializer {
   }
 
   async ensureSettingsFileExists(): Promise<void> {
-    // Only create if it doesn't exist
     if (await fs.pathExists(this.settingsFilePath)) {
+      await this.applyMissingDefaults();
       return;
     }
 
@@ -70,6 +73,20 @@ export class FsSettingsInitializer implements ISettingsInitializer {
     await fs.writeFile(this.settingsFilePath, content, "utf-8");
   }
 
+  /**
+   * Fill in any missing default sections or fields on an existing settings
+   * file, leaving explicit values and unknown entries untouched.
+   */
+  private async applyMissingDefaults(): Promise<void> {
+    const content = await fs.readFile(this.settingsFilePath, "utf-8");
+    assertValidJsonc(content, this.settingsFilePath);
+
+    const updated = applyMissingDefaults(content, DEFAULT_SETTINGS as unknown as JsonObject);
+    if (updated !== content) {
+      await fs.writeFile(this.settingsFilePath, updated, "utf-8");
+    }
+  }
+
   async getPlannedFileChange(): Promise<PlannedFileChange | null> {
     if (await fs.pathExists(this.settingsFilePath)) {
       return null; // No change needed
diff --git a/src/infrastructure/settings/FsSettingsReader.ts b/src/infrastructure/settings/FsSettingsReader.ts
index 5965478a..48dc643d 100644
--- a/src/infrastructure/settings/FsSettingsReader.ts
+++ b/src/infrastructure/settings/FsSettingsReader.ts
@@ -4,6 +4,7 @@ import * as jsonc from "jsonc-parser";
 import { ISettingsReader } from "../../application/settings/ISettingsReader.js";
 import { Settings } from "../../application/settings/Settings.js";
 import { DEFAULT_SETTINGS } from "./DefaultSettings.js";
+import { JsonValue, setJsoncValue } from "./JsoncSettingsEditor.js";
 
 /**
  * JsoncSettingsReader - File system implementation for reading settings.
@@ -55,8 +56,56 @@ export class FsSettingsReader implements ISettingsReader {
 
   async write(settings: Settings): Promise<void> {
     const normalizedSettings = this.mergeWithDefaults(settings);
-    const content = this.buildSettingsFileContent(normalizedSettings);
-    await fs.writeFile(this.settingsFilePath, content, "utf-8");
+
+    if (!(await fs.pathExists(this.settingsFilePath))) {
+      const content = this.buildSettingsFileContent(normalizedSettings);
+      await fs.writeFile(this.settingsFilePath, content, "utf-8");
+      return;
+    }
+
+    const existingContent = await fs.readFile(this.settingsFilePath, "utf-8");
+    const errors: jsonc.ParseError[] = [];
+    jsonc.parse(existingContent, errors, { allowTrailingComma: true });
+    if (errors.length > 0) {
+      throw new Error(
+        `Invalid JSON in settings file: ${this.formatParseErrors(errors)}`
+      );
+    }
+
+    let updated = existingContent;
+    for (const { path: fieldPath, value } of this.knownValueEntries(normalizedSettings)) {
+      updated = setJsoncValue(updated, fieldPath, value);
+    }
+    await fs.writeFile(this.settingsFilePath, updated, "utf-8");
+  }
+
+  /**
+   * Known settings leaf paths and their values, used to persist changes onto
+   * an existing settings file without disturbing unknown entries elsewhere
+   * in the document.
+   */
+  private knownValueEntries(
+    settings: Settings
+  ): Array<{ path: jsonc.JSONPath; value: JsonValue }> {
+    return [
+      { path: ["project", "id"], value: settings.project!.id },
+      { path: ["qa", "defaultTurnLimit"], value: settings.qa.defaultTurnLimit },
+      {
+        path: ["claims", "claimDurationMinutes"],
+        value: settings.claims.claimDurationMinutes,
+      },
+      { path: ["telemetry", "enabled"], value: settings.telemetry.enabled },
+      { path: ["telemetry", "anonymousId"], value: settings.telemetry.anonymousId },
+      { path: ["telemetry", "consentGiven"], value: settings.telemetry.consentGiven },
+      {
+        path: ["tui", "showLaunchpadWelcome"],
+        value: settings.tui!.showLaunchpadWelcome,
+      },
+      {
+        path: ["session", "backlogPreviewSize"],
+        value: settings.session!.backlogPreviewSize,
+      },
+    ];
   }
 
   async hasTelemetryConfiguration(): Promise<boolean> {
diff --git a/src/infrastructure/settings/JsoncSettingsEditor.ts b/src/infrastructure/settings/JsoncSettingsEditor.ts
new file mode 100644
index 00000000..ae61f68d
--- /dev/null
+++ b/src/infrastructure/settings/JsoncSettingsEditor.ts
@@ -0,0 +1,101 @@
+import * as jsonc from "jsonc-parser";
+
+/**
+ * Recursive JSON value shape used to walk settings documents and defaults
+ * without resorting to `any` at the JSONC editing boundary.
+ */
+export type JsonValue =
+  | string
+  | number
+  | boolean
+  | null
+  | JsonValue[]
+  | { [key: string]: JsonValue };
+
+export type JsonObject = { [key: string]: JsonValue };
+
+const FORMATTING_OPTIONS: jsonc.FormattingOptions = {
+  insertSpaces: true,
+  tabSize: 2,
+  eol: "\n",
+};
+
+function isPlainObject(value: JsonValue): value is JsonObject {
+  return typeof value === "object" && value !== null && !Array.isArray(value);
+}
+
+/**
+ * Parse settings JSONC content, throwing a descriptive error if it is invalid.
+ * Used at every write path so malformed files fail loudly instead of being
+ * partially rewritten.
+ */
+export function assertValidJsonc(content: string, filePath: string): void {
+  const errors: jsonc.ParseError[] = [];
+  jsonc.parse(content, errors, { allowTrailingComma: true });
+  if (errors.length > 0) {
+    const formatted = errors
+      .map((err) => `Error at offset ${err.offset}: ${jsonc.printParseErrorCode(err.error)}`)
+      .join(", ");
+    throw new Error(`Invalid JSON in settings file at ${filePath}: ${formatted}`);
+  }
+}
+
+/**
+ * Set a single value at `path` within JSONC `content`, preserving comments,
+ * formatting, and every other entry in the document.
+ */
+export function setJsoncValue(content: string, path: jsonc.JSONPath, value: JsonValue): string {
+  const edits = jsonc.modify(content, path, value, { formattingOptions: FORMATTING_OPTIONS });
+  return jsonc.applyEdits(content, edits);
+}
+
+function isMissing(content: string, path: jsonc.JSONPath): boolean {
+  const tree = jsonc.parseTree(content);
+  if (!tree) {
+    return true;
+  }
+  return jsonc.findNodeAtLocation(tree, path) === undefined;
+}
+
+export interface MissingEntry {
+  path: jsonc.JSONPath;
+  value: JsonValue;
+}
+
+/**
+ * Walk `defaults` against existing JSONC `content` and collect entries that
+ * are absent. Whole subtrees are reported as a single entry when their parent
+ * is entirely missing; otherwise only the missing nested fields are reported.
+ * Collected entries never nest one inside another, so they can be applied to
+ * `content` in any order without conflicting.
+ */
+export function collectMissingDefaults(
+  content: string,
+  defaults: JsonObject,
+  basePath: jsonc.JSONPath = []
+): MissingEntry[] {
+  const entries: MissingEntry[] = [];
+  for (const key of Object.keys(defaults)) {
+    const path = [...basePath, key];
+    const value = defaults[key];
+    if (isMissing(content, path)) {
+      entries.push({ path, value });
+    } else if (isPlainObject(value)) {
+      entries.push(...collectMissingDefaults(content, value, path));
+    }
+  }
+  return entries;
+}
+
+/**
+ * Apply every missing default entry to `content`, returning the updated
+ * document. Returns `content` unchanged if there is nothing to add.
+ */
+export function applyMissingDefaults(content: string, defaults: JsonObject): string {
+  const entries = collectMissingDefaults(content, defaults);
+  let updated = content;
+  for (const entry of entries) {
+    updated = setJsoncValue(updated, entry.path, entry.value);
+  }
+  return updated;
+}
diff --git a/tests/infrastructure/settings/FsSettingsInitializer.test.ts b/tests/infrastructure/settings/FsSettingsInitializer.test.ts
index a8802928..e21763bf 100644
--- a/tests/infrastructure/settings/FsSettingsInitializer.test.ts
+++ b/tests/infrastructure/settings/FsSettingsInitializer.test.ts
@@ -38,4 +38,94 @@ describe("FsSettingsInitializer", () => {
     const settings = await new FsSettingsReader(tempDir).read();
     expect(settings.session).toEqual(DEFAULT_SETTINGS.session);
   });
+
+  it("adds missing default sections to an existing settings file", async () => {
+    const tempDir = await createTempDir();
+    const settingsPath = path.join(tempDir, "settings.jsonc");
+    await fs.writeFile(
+      settingsPath,
+      JSON.stringify({
+        qa: { defaultTurnLimit: 7 },
+        claims: { claimDurationMinutes: 45 },
+        telemetry: { enabled: false, anonymousId: null, consentGiven: true },
+      }),
+      "utf-8",
+    );
+    const initializer = new FsSettingsInitializer(tempDir);
+
+    await initializer.ensureSettingsFileExists();
+
+    const settings = await new FsSettingsReader(tempDir).read();
+    expect(settings.project).toEqual(DEFAULT_SETTINGS.project);
+    expect(settings.tui).toEqual(DEFAULT_SETTINGS.tui);
+    expect(settings.session).toEqual(DEFAULT_SETTINGS.session);
+  });
+
+  it("preserves explicit known values already present in the settings file", async () => {
+    const tempDir = await createTempDir();
+    const settingsPath = path.join(tempDir, "settings.jsonc");
+    await fs.writeFile(
+      settingsPath,
+      JSON.stringify({
+        project: { id: "11111111-1111-4111-8111-111111111111" },
+        qa: { defaultTurnLimit: 7 },
+        claims: { claimDurationMinutes: 45 },
+        telemetry: { enabled: false, anonymousId: null, consentGiven: true },
+        tui: { showLaunchpadWelcome: false },
+        session: { backlogPreviewSize: 2 },
+      }),
+      "utf-8",
+    );
+    const initializer = new FsSettingsInitializer(tempDir);
+
+    await initializer.ensureSettingsFileExists();
+
+    const settings = await new FsSettingsReader(tempDir).read();
+    expect(settings.project).toEqual({ id: "11111111-1111-4111-8111-111111111111" });
+    expect(settings.qa).toEqual({ defaultTurnLimit: 7 });
+    expect(settings.claims).toEqual({ claimDurationMinutes: 45 });
+    expect(settings.telemetry).toEqual({ enabled: false, anonymousId: null, consentGiven: true });
+    expect(settings.tui).toEqual({ showLaunchpadWelcome: false });
+    expect(settings.session).toEqual({ backlogPreviewSize: 2 });
+  });
+
+  it("preserves unknown top-level and nested entries when filling in defaults", async () => {
+    const tempDir = await createTempDir();
+    const settingsPath = path.join(tempDir, "settings.jsonc");
+    await fs.writeFile(
+      settingsPath,
+      JSON.stringify({
+        qa: { defaultTurnLimit: 7, customField: "keep-me" },
+        claims: { claimDurationMinutes: 45 },
+        telemetry: { enabled: false, anonymousId: null, consentGiven: true },
+        experimental: { flagA: true },
+      }),
+      "utf-8",
+    );
+    const initializer = new FsSettingsInitializer(tempDir);
+
+    await initializer.ensureSettingsFileExists();
+
+    const rawContent = await fs.readFile(settingsPath, "utf-8");
+    const raw = JSON.parse(
+      rawContent
+        .split("\n")
+        .filter((line) => !line.trim().startsWith("//"))
+        .join("\n"),
+    );
+    expect(raw.qa.customField).toBe("keep-me");
+    expect(raw.experimental).toEqual({ flagA: true });
+  });
+
+  it("throws a clear error instead of rewriting an invalid JSONC settings file", async () => {
+    const tempDir = await createTempDir();
+    const settingsPath = path.join(tempDir, "settings.jsonc");
+    await fs.writeFile(settingsPath, "{ invalid json ", "utf-8");
+    const initializer = new FsSettingsInitializer(tempDir);
+
+    await expect(initializer.ensureSettingsFileExists()).rejects.toThrow();
+
+    const contentAfterFailure = await fs.readFile(settingsPath, "utf-8");
+    expect(contentAfterFailure).toBe("{ invalid json ");
+  });
 });
diff --git a/tests/infrastructure/settings/FsSettingsReader.test.ts b/tests/infrastructure/settings/FsSettingsReader.test.ts
index 257ac7ce..acdb0f04 100644
--- a/tests/infrastructure/settings/FsSettingsReader.test.ts
+++ b/tests/infrastructure/settings/FsSettingsReader.test.ts
@@ -117,4 +117,32 @@ describe("FsSettingsReader", () => {
       session: { backlogPreviewSize: 2 },
     });
   });
+
+  it("preserves unknown top-level and nested entries when persisting known settings changes", async () => {
+    const tempDir = await createTempDir();
+    const settingsPath = path.join(tempDir, "settings.jsonc");
+    await fs.writeFile(
+      settingsPath,
+      JSON.stringify({
+        ...DEFAULT_SETTINGS,
+        qa: { defaultTurnLimit: 3, customField: "keep-me" },
+        experimental: { flagA: true },
+      }),
+      "utf-8",
+    );
+    const reader = new FsSettingsReader(tempDir);
+
+    await reader.write({
+      ...DEFAULT_SETTINGS,
+      tui: { showLaunchpadWelcome: false },
+    });
+
+    const rawContent = await fs.readFile(settingsPath, "utf-8");
+    const raw = JSON.parse(rawContent);
+    expect(raw.qa.customField).toBe("keep-me");
+    expect(raw.experimental).toEqual({ flagA: true });
+
+    const settings = await reader.read();
+    expect(settings.tui).toEqual({ showLaunchpadWelcome: false });
+  });
 });
diff --git a/tests/infrastructure/settings/JsoncSettingsEditor.test.ts b/tests/infrastructure/settings/JsoncSettingsEditor.test.ts
new file mode 100644
index 00000000..b8eda578
--- /dev/null
+++ b/tests/infrastructure/settings/JsoncSettingsEditor.test.ts
@@ -0,0 +1,127 @@
+import { describe, expect, it } from "@jest/globals";
+import {
+  JsonObject,
+  applyMissingDefaults,
+  assertValidJsonc,
+  collectMissingDefaults,
+  setJsoncValue,
+} from "../../../src/infrastructure/settings/JsoncSettingsEditor.js";
+
+describe("JsoncSettingsEditor", () => {
+  describe("assertValidJsonc", () => {
+    it("does not throw for valid JSONC content", () => {
+      expect(() => assertValidJsonc('{ "a": 1 }', "settings.jsonc")).not.toThrow();
+    });
+
+    it("throws a descriptive error for invalid JSONC content", () => {
+      expect(() => assertValidJsonc("{ invalid", "settings.jsonc")).toThrow(
+        /Invalid JSON in settings file at settings\.jsonc/
+      );
+    });
+  });
+
+  describe("setJsoncValue", () => {
+    it("sets a nested value while preserving comments and unrelated entries", () => {
+      const content = `{
+  // keep this comment
+  "qa": {
+    "defaultTurnLimit": 3
+  },
+  "custom": {
+    "flag": true
+  }
+}
+`;
+
+      const updated = setJsoncValue(content, ["qa", "defaultTurnLimit"], 9);
+
+      expect(updated).toContain("// keep this comment");
+      expect(JSON.parse(updated.replace(/\/\/.*$/gm, ""))).toEqual({
+        qa: { defaultTurnLimit: 9 },
+        custom: { flag: true },
+      });
+    });
+
+    it("inserts a value at a path that does not yet exist", () => {
+      const content = `{
+  "qa": { "defaultTurnLimit": 3 }
+}
+`;
+
+      const updated = setJsoncValue(content, ["tui", "showLaunchpadWelcome"], false);
+
+      expect(JSON.parse(updated)).toEqual({
+        qa: { defaultTurnLimit: 3 },
+        tui: { showLaunchpadWelcome: false },
+      });
+    });
+  });
+
+  describe("collectMissingDefaults", () => {
+    it("reports an entire section as missing when its parent key is absent", () => {
+      const content = `{ "qa": { "defaultTurnLimit": 3 } }`;
+      const defaults: JsonObject = {
+        qa: { defaultTurnLimit: 3 },
+        tui: { showLaunchpadWelcome: true },
+      };
+
+      const entries = collectMissingDefaults(content, defaults);
+
+      expect(entries).toEqual([{ path: ["tui"], value: { showLaunchpadWelcome: true } }]);
+    });
+
+    it("reports only the missing nested field when the parent already exists", () => {
+      const content = `{ "telemetry": { "enabled": false } }`;
+      const defaults: JsonObject = {
+        telemetry: { enabled: true, anonymousId: null, consentGiven: false },
+      };
+
+      const entries = collectMissingDefaults(content, defaults);
+
+      expect(entries).toEqual(
+        expect.arrayContaining([
+          { path: ["telemetry", "anonymousId"], value: null },
+          { path: ["telemetry", "consentGiven"], value: false },
+        ])
+      );
+      expect(entries).toHaveLength(2);
+    });
+
+    it("reports nothing missing when every default field is already present", () => {
+      const content = `{ "qa": { "defaultTurnLimit": 3 } }`;
+      const defaults: JsonObject = { qa: { defaultTurnLimit: 3 } };
+
+      expect(collectMissingDefaults(content, defaults)).toEqual([]);
+    });
+  });
+
+  describe("applyMissingDefaults", () => {
+    it("adds missing sections and fields without overwriting explicit values", () => {
+      const content = `{
+  "qa": { "defaultTurnLimit": 7 },
+  "custom": { "keep": true }
+}
+`;
+      const defaults: JsonObject = {
+        qa: { defaultTurnLimit: 3 },
+        tui: { showLaunchpadWelcome: true },
+        session: { backlogPreviewSize: 5 },
+      };
+
+      const updated = applyMissingDefaults(content, defaults);
+      const parsed = JSON.parse(updated);
+
+      expect(parsed.qa).toEqual({ defaultTurnLimit: 7 });
+      expect(parsed.custom).toEqual({ keep: true });
+      expect(parsed.tui).toEqual({ showLaunchpadWelcome: true });
+      expect(parsed.session).toEqual({ backlogPreviewSize: 5 });
+    });
+
+    it("returns the content unchanged when nothing is missing", () => {
+      const content = `{ "qa": { "defaultTurnLimit": 3 } }`;
+      const defaults: JsonObject = { qa: { defaultTurnLimit: 3 } };
+
+      expect(applyMissingDefaults(content, defaults)).toBe(content);
+    });
+  });
+});