diff --git a/src/commands/init.ts b/src/commands/init.ts
index ec30e840..1cb8a599 100644
--- a/src/commands/init.ts
+++ b/src/commands/init.ts
@@ -2,7 +2,10 @@ import type { Command } from 'commander';
 import type { IOutputFormatter } from '../interfaces/output-formatter.js';
 import { mkdir, readFile, writeFile, access } from 'node:fs/promises';
 import { join } from 'node:path';
+import { parse as parseToml } from 'smol-toml';
 import { CONFIG_DIR, CONFIG_FILENAME } from '../util/constants.js';
+import { DEFAULT_CONFIG, type LoreConfig } from '../types/config.js';
+import { LoreError } from '../util/errors.js';
 
 const DEFAULT_CONFIG_CONTENT = `[protocol]
 version = "1.0"
@@ -33,7 +36,7 @@ update_check = true
 /**
  * Register the `lore init` command.
  * Creates .lore/config.toml with default content.
- * If the config file already exists, prints its content and exits.
+ * If the config file already exists, checks for corruption and missing options.
  */
 export function registerInitCommand(
   program: Command,
@@ -64,6 +67,37 @@ export function registerInitCommand(
           `Config already exists at ${CONFIG_DIR}/${CONFIG_FILENAME}:`,
         ));
         console.log(content);
+
+        let parsed: Record<string, unknown>;
+        try {
+          parsed = parseToml(content) as Record<string, unknown>;
+        } catch (err) {
+          const message = `Your configuration file is corrupted and cannot be parsed: ${err instanceof Error ? err.message : String(err)}\n\nPlease fix the TOML syntax or reset your config.\nExample: mv ${CONFIG_DIR}/${CONFIG_FILENAME} ${CONFIG_DIR}/${CONFIG_FILENAME}.corrupted && lore init`;
+          throw new LoreError(message, 1);
+        }
+
+        const { missing, customized } = findConfigDiff(parsed);
+
+        if (missing.length > 0) {
+          console.log('\n' + formatter.formatSuccess(
+            'Your configuration is missing new options:',
+          ));
+          for (const item of missing) {
+            console.log(`  - ${item}`);
+          }
+
+          if (customized.length === 0) {
+            console.log('\nNotice: You are using default settings. You can safely reset your config to get the latest options.');
+            console.log(`Example: rm ${CONFIG_DIR}/${CONFIG_FILENAME} && lore init`);
+          } else {
+            console.log('\nNotice: You have customized the following options:');
+            for (const item of customized) {
+              console.log(`  - ${item}`);
+            }
+            console.log('\nTo update: Rename your current config, run `lore init` again, and manually merge your changes.');
+            console.log(`Example: mv ${CONFIG_DIR}/${CONFIG_FILENAME} ${CONFIG_DIR}/${CONFIG_FILENAME}.bak && lore init`);
+          }
+        }
         return;
       }
 
@@ -76,3 +110,36 @@ export function registerInitCommand(
       ));
     });
 }
+
+function findConfigDiff(parsed: Record<string, unknown>): { missing: string[]; customized: string[] } {
+  const missing: string[] = [];
+  const customized: string[] = [];
+
+  const configKeys = Object.keys(DEFAULT_CONFIG) as (keyof LoreConfig)[];
+
+  for (const section of configKeys) {
+    const defaults = DEFAULT_CONFIG[section] as Record<string, unknown>;
+    const userSection = parsed[section];
+
+    if (!userSection || typeof userSection !== 'object') {
+      missing.push(`[${section}] section`);
+      continue;
+    }
+
+    const sectionData = userSection as Record<string, unknown>;
+    for (const [key, defaultValue] of Object.entries(defaults)) {
+      // Convert camelCase from LoreConfig type to snake_case for TOML comparison
+      const snakeKey = key.replace(/[A-Z]/g, letter => `_${letter.toLowerCase()}`);
+      const userValue = sectionData[snakeKey] ?? sectionData[key];
+
+      if (userValue === undefined) {
+        missing.push(`${section}.${snakeKey}`);
+      } else if (JSON.stringify(userValue) !== JSON.stringify(defaultValue)) {
+        customized.push(`${section}.${snakeKey}`);
+      }
+    }
+  }
+
+  return { missing, customized };
+}
+
diff --git a/tests/unit/commands/init.test.ts b/tests/unit/commands/init.test.ts
new file mode 100644
index 00000000..f039f2e7
--- /dev/null
+++ b/tests/unit/commands/init.test.ts
@@ -0,0 +1,172 @@
+import { describe, it, expect, vi, beforeEach, afterEach } from 'vitest';
+import { Command } from 'commander';
+import { registerInitCommand } from '../../../src/commands/init.js';
+import type { IOutputFormatter } from '../../../src/interfaces/output-formatter.js';
+import * as fs from 'node:fs/promises';
+import { join } from 'node:path';
+import { CONFIG_DIR, CONFIG_FILENAME } from '../../../src/util/constants.js';
+
+vi.mock('node:fs/promises');
+
+describe('registerInitCommand', () => {
+  const formatter: IOutputFormatter = {
+    formatSuccess: vi.fn((msg) => `SUCCESS: ${msg}`),
+    formatError: vi.fn((code, messages) => `ERROR: ${messages[0].message} (code ${code})`),
+    formatQueryResult: vi.fn(),
+    formatValidationResult: vi.fn(),
+    formatStalenessResult: vi.fn(),
+    formatTraceResult: vi.fn(),
+    formatDoctorResult: vi.fn(),
+  };
+
+  let consoleLogSpy: any;
+
+  beforeEach(() => {
+    vi.clearAllMocks();
+    consoleLogSpy = vi.spyOn(console, 'log').mockImplementation(() => {});
+    // Default: file does not exist
+    vi.mocked(fs.access).mockRejectedValue(new Error('ENOENT'));
+  });
+
+  afterEach(() => {
+    consoleLogSpy.mockRestore();
+  });
+
+  it('creates a new config file if one does not exist', async () => {
+    const program = new Command();
+    registerInitCommand(program, { getFormatter: () => formatter });
+
+    await program.parseAsync(['node', 'lore', 'init']);
+
+    expect(fs.mkdir).toHaveBeenCalledWith(expect.stringContaining(CONFIG_DIR), { recursive: true });
+    expect(fs.writeFile).toHaveBeenCalledWith(
+      expect.stringContaining(join(CONFIG_DIR, CONFIG_FILENAME)),
+      expect.stringContaining('[protocol]'),
+      'utf-8'
+    );
+    expect(consoleLogSpy).toHaveBeenCalledWith(expect.stringContaining('Created .lore/config.toml'));
+  });
+
+  it('reports an existing valid config with no gaps', async () => {
+    const fullConfig = `[protocol]
+version = "1.0"
+[trailers]
+required = []
+custom = []
+[validation]
+strict = false
+max_message_lines = 50
+intent_max_length = 72
+[stale]
+older_than = "6m"
+drift_threshold = 20
+[output]
+default_format = "text"
+[follow]
+max_depth = 3
+[cli]
+update_check = true
+`;
+    vi.mocked(fs.access).mockResolvedValue(undefined);
+    vi.mocked(fs.readFile).mockResolvedValue(fullConfig);
+
+    const program = new Command();
+    registerInitCommand(program, { getFormatter: () => formatter });
+
+    await program.parseAsync(['node', 'lore', 'init']);
+
+    expect(fs.writeFile).not.toHaveBeenCalled();
+    expect(consoleLogSpy).toHaveBeenCalledWith(expect.stringContaining('Config already exists'));
+    // Should NOT have warning about missing options
+    expect(consoleLogSpy).not.toHaveBeenCalledWith(expect.stringContaining('WARNING: Your configuration is missing new options:'));
+  });
+
+  it('reports missing options and suggests safe reset if no customizations exist', async () => {
+    const minimalConfig = `[protocol]
+  version = "1.0"
+  `;
+    vi.mocked(fs.access).mockResolvedValue(undefined);
+    vi.mocked(fs.readFile).mockResolvedValue(minimalConfig);
+
+    const program = new Command();
+    registerInitCommand(program, { getFormatter: () => formatter });
+
+    await program.parseAsync(['node', 'lore', 'init']);
+
+    expect(consoleLogSpy).toHaveBeenCalledWith(expect.stringContaining('SUCCESS: Your configuration is missing new options:'));
+    expect(consoleLogSpy).toHaveBeenCalledWith(expect.stringContaining('- [trailers] section'));
+    expect(consoleLogSpy).toHaveBeenCalledWith(expect.stringContaining('Notice: You are using default settings. You can safely reset your config'));
+    expect(consoleLogSpy).toHaveBeenCalledWith(expect.stringContaining('rm .lore/config.toml && lore init'));
+  });
+
+  it('reports missing options and suggests manual merge if customizations exist', async () => {
+    const customizedConfig = `[protocol]
+  version = "1.0"
+  [validation]
+  strict = true
+  `;
+    vi.mocked(fs.access).mockResolvedValue(undefined);
+    vi.mocked(fs.readFile).mockResolvedValue(customizedConfig);
+
+    const program = new Command();
+    registerInitCommand(program, { getFormatter: () => formatter });
+
+    await program.parseAsync(['node', 'lore', 'init']);
+
+    expect(consoleLogSpy).toHaveBeenCalledWith(expect.stringContaining('SUCCESS: Your configuration is missing new options:'));
+    expect(consoleLogSpy).toHaveBeenCalledWith(expect.stringContaining('- [trailers] section'));
+    expect(consoleLogSpy).toHaveBeenCalledWith(expect.stringContaining('Notice: You have customized the following options:'));
+    expect(consoleLogSpy).toHaveBeenCalledWith(expect.stringContaining('- validation.strict'));
+    expect(consoleLogSpy).toHaveBeenCalledWith(expect.stringContaining('To update: Rename your current config'));
+  });
+
+  it('reports individual missing keys when section exists', async () => {
+
+    const configWithMissingKey = `[protocol]
+    version = "1.0"
+    [trailers]
+    required = []
+    custom = []
+    [validation]
+    strict = false
+    max_message_lines = 50
+    intent_max_length = 72
+    [stale]
+    older_than = "6m"
+    drift_threshold = 20
+    [output]
+    default_format = "text"
+    [follow]
+    # max_depth is missing
+    [cli]
+    update_check = true
+    `;
+    vi.mocked(fs.access).mockResolvedValue(undefined);
+    vi.mocked(fs.readFile).mockResolvedValue(configWithMissingKey);
+
+    const program = new Command();
+    registerInitCommand(program, { getFormatter: () => formatter });
+
+    await program.parseAsync(['node', 'lore', 'init']);
+
+    expect(consoleLogSpy).toHaveBeenCalledWith(expect.stringContaining('SUCCESS: Your configuration is missing new options:'));
+    expect(consoleLogSpy).toHaveBeenCalledWith(expect.stringContaining('- follow.max_depth'));
+    });
+
+    it('reports corruption if the existing config is invalid TOML', async () => {
+      const corruptedConfig = `[protocol]
+    version = "1.0
+    invalid = [missing bracket
+    `;
+      vi.mocked(fs.access).mockResolvedValue(undefined);
+      vi.mocked(fs.readFile).mockResolvedValue(corruptedConfig);
+
+      const program = new Command();
+      program.exitOverride();
+      registerInitCommand(program, { getFormatter: () => formatter });
+
+      await expect(program.parseAsync(['node', 'lore', 'init']))
+        .rejects.toThrow(/Your configuration file is corrupted/);
+    });
+
+});