diff --git a/src/cli/src/commands/claude.ts b/src/cli/src/commands/claude.ts
new file mode 100644
index 0000000..6756037
--- /dev/null
+++ b/src/cli/src/commands/claude.ts
@@ -0,0 +1,155 @@
+import { Command } from 'commander';
+import { writeFileSync, readFileSync, existsSync } from 'node:fs';
+import { resolve } from 'node:path';
+import type { ApiClient } from '../api-client.js';
+
+interface McpConfig {
+  mcpServers: Record<string, { command: string; args: string[]; env?: Record<string, string> }>;
+}
+
+export interface ClaudeCommandDeps {
+  client: ApiClient;
+  log: (...args: unknown[]) => void;
+}
+
+export function createClaudeCommand(deps: ClaudeCommandDeps): Command {
+  const { client, log } = deps;
+
+  const cmd = new Command('claude')
+    .description('Manage Claude MCP configuration (.mcp.json)');
+
+  cmd
+    .command('generate <projectId>')
+    .description('Generate .mcp.json from a project configuration')
+    .option('-o, --output <path>', 'Output file path', '.mcp.json')
+    .option('--merge', 'Merge with existing .mcp.json instead of overwriting')
+    .option('--stdout', 'Print to stdout instead of writing a file')
+    .action(async (projectId: string, opts: { output: string; merge?: boolean; stdout?: boolean }) => {
+      const config = await client.get<McpConfig>(`/api/v1/projects/${projectId}/mcp-config`);
+
+      if (opts.stdout) {
+        log(JSON.stringify(config, null, 2));
+        return;
+      }
+
+      const outputPath = resolve(opts.output);
+      let finalConfig = config;
+
+      if (opts.merge && existsSync(outputPath)) {
+        try {
+          const existing = JSON.parse(readFileSync(outputPath, 'utf-8')) as McpConfig;
+          finalConfig = {
+            mcpServers: {
+              ...existing.mcpServers,
+              ...config.mcpServers,
+            },
+          };
+        } catch {
+          // If existing file is invalid, just overwrite
+        }
+      }
+
+      writeFileSync(outputPath, JSON.stringify(finalConfig, null, 2) + '\n');
+      const serverCount = Object.keys(finalConfig.mcpServers).length;
+      log(`Wrote ${outputPath} (${serverCount} server(s))`);
+    });
+
+  cmd
+    .command('show')
+    .description('Show current .mcp.json configuration')
+    .option('-p, --path <path>', 'Path to .mcp.json', '.mcp.json')
+    .action((opts: { path: string }) => {
+      const filePath = resolve(opts.path);
+      if (!existsSync(filePath)) {
+        log(`No .mcp.json found at ${filePath}`);
+        return;
+      }
+      const content = readFileSync(filePath, 'utf-8');
+      try {
+        const config = JSON.parse(content) as McpConfig;
+        const servers = Object.entries(config.mcpServers ?? {});
+        if (servers.length === 0) {
+          log('No MCP servers configured.');
+          return;
+        }
+        log(`MCP servers in ${filePath}:\n`);
+        for (const [name, server] of servers) {
+          log(`  ${name}`);
+          log(`    command: ${server.command} ${server.args.join(' ')}`);
+          if (server.env) {
+            const envKeys = Object.keys(server.env);
+            log(`    env: ${envKeys.join(', ')}`);
+          }
+        }
+      } catch {
+        log(`Invalid JSON in ${filePath}`);
+      }
+    });
+
+  cmd
+    .command('add <name>')
+    .description('Add an MCP server entry to .mcp.json')
+    .requiredOption('-c, --command <cmd>', 'Command to run')
+    .option('-a, --args <args...>', 'Command arguments')
+    .option('-e, --env <key=value...>', 'Environment variables')
+    .option('-p, --path <path>', 'Path to .mcp.json', '.mcp.json')
+    .action((name: string, opts: { command: string; args?: string[]; env?: string[]; path: string }) => {
+      const filePath = resolve(opts.path);
+      let config: McpConfig = { mcpServers: {} };
+
+      if (existsSync(filePath)) {
+        try {
+          config = JSON.parse(readFileSync(filePath, 'utf-8')) as McpConfig;
+        } catch {
+          // Start fresh
+        }
+      }
+
+      const entry: { command: string; args: string[]; env?: Record<string, string> } = {
+        command: opts.command,
+        args: opts.args ?? [],
+      };
+
+      if (opts.env && opts.env.length > 0) {
+        const env: Record<string, string> = {};
+        for (const pair of opts.env) {
+          const eqIdx = pair.indexOf('=');
+          if (eqIdx > 0) {
+            env[pair.slice(0, eqIdx)] = pair.slice(eqIdx + 1);
+          }
+        }
+        entry.env = env;
+      }
+
+      config.mcpServers[name] = entry;
+      writeFileSync(filePath, JSON.stringify(config, null, 2) + '\n');
+      log(`Added '${name}' to ${filePath}`);
+    });
+
+  cmd
+    .command('remove <name>')
+    .description('Remove an MCP server entry from .mcp.json')
+    .option('-p, --path <path>', 'Path to .mcp.json', '.mcp.json')
+    .action((name: string, opts: { path: string }) => {
+      const filePath = resolve(opts.path);
+      if (!existsSync(filePath)) {
+        log(`No .mcp.json found at ${filePath}`);
+        return;
+      }
+
+      try {
+        const config = JSON.parse(readFileSync(filePath, 'utf-8')) as McpConfig;
+        if (!(name in config.mcpServers)) {
+          log(`Server '${name}' not found in ${filePath}`);
+          return;
+        }
+        delete config.mcpServers[name];
+        writeFileSync(filePath, JSON.stringify(config, null, 2) + '\n');
+        log(`Removed '${name}' from ${filePath}`);
+      } catch {
+        log(`Invalid JSON in ${filePath}`);
+      }
+    });
+
+  return cmd;
+}
diff --git a/src/cli/src/commands/project.ts b/src/cli/src/commands/project.ts
new file mode 100644
index 0000000..275a111
--- /dev/null
+++ b/src/cli/src/commands/project.ts
@@ -0,0 +1,129 @@
+import { Command } from 'commander';
+import type { ApiClient } from '../api-client.js';
+
+interface Project {
+  id: string;
+  name: string;
+  description: string;
+  ownerId: string;
+  createdAt: string;
+}
+
+interface Profile {
+  id: string;
+  name: string;
+  serverId: string;
+}
+
+export interface ProjectCommandDeps {
+  client: ApiClient;
+  log: (...args: unknown[]) => void;
+}
+
+export function createProjectCommand(deps: ProjectCommandDeps): Command {
+  const { client, log } = deps;
+
+  const cmd = new Command('project')
+    .alias('projects')
+    .alias('proj')
+    .description('Manage mcpctl projects');
+
+  cmd
+    .command('list')
+    .alias('ls')
+    .description('List all projects')
+    .option('-o, --output <format>', 'Output format (table, json)', 'table')
+    .action(async (opts: { output: string }) => {
+      const projects = await client.get<Project[]>('/api/v1/projects');
+      if (opts.output === 'json') {
+        log(JSON.stringify(projects, null, 2));
+        return;
+      }
+      if (projects.length === 0) {
+        log('No projects found.');
+        return;
+      }
+      log('ID\tNAME\tDESCRIPTION');
+      for (const p of projects) {
+        log(`${p.id}\t${p.name}\t${p.description || '-'}`);
+      }
+    });
+
+  cmd
+    .command('create <name>')
+    .description('Create a new project')
+    .option('-d, --description <text>', 'Project description', '')
+    .action(async (name: string, opts: { description: string }) => {
+      const project = await client.post<Project>('/api/v1/projects', {
+        name,
+        description: opts.description,
+      });
+      log(`Project '${project.name}' created (id: ${project.id})`);
+    });
+
+  cmd
+    .command('delete <id>')
+    .alias('rm')
+    .description('Delete a project')
+    .action(async (id: string) => {
+      await client.delete(`/api/v1/projects/${id}`);
+      log(`Project '${id}' deleted.`);
+    });
+
+  cmd
+    .command('show <id>')
+    .description('Show project details')
+    .action(async (id: string) => {
+      const project = await client.get<Project>(`/api/v1/projects/${id}`);
+      log(`Name: ${project.name}`);
+      log(`ID: ${project.id}`);
+      log(`Description: ${project.description || '-'}`);
+      log(`Owner: ${project.ownerId}`);
+      log(`Created: ${project.createdAt}`);
+
+      try {
+        const profiles = await client.get<Profile[]>(`/api/v1/projects/${id}/profiles`);
+        if (profiles.length > 0) {
+          log('\nProfiles:');
+          for (const p of profiles) {
+            log(`  - ${p.name} (id: ${p.id})`);
+          }
+        } else {
+          log('\nNo profiles assigned.');
+        }
+      } catch {
+        // Profiles endpoint may not be available
+      }
+    });
+
+  cmd
+    .command('profiles <id>')
+    .description('List profiles assigned to a project')
+    .option('-o, --output <format>', 'Output format (table, json)', 'table')
+    .action(async (id: string, opts: { output: string }) => {
+      const profiles = await client.get<Profile[]>(`/api/v1/projects/${id}/profiles`);
+      if (opts.output === 'json') {
+        log(JSON.stringify(profiles, null, 2));
+        return;
+      }
+      if (profiles.length === 0) {
+        log('No profiles assigned.');
+        return;
+      }
+      log('ID\tNAME\tSERVER');
+      for (const p of profiles) {
+        log(`${p.id}\t${p.name}\t${p.serverId}`);
+      }
+    });
+
+  cmd
+    .command('set-profiles <id>')
+    .description('Set the profiles assigned to a project')
+    .argument('<profileIds...>', 'Profile IDs to assign')
+    .action(async (id: string, profileIds: string[]) => {
+      await client.put(`/api/v1/projects/${id}/profiles`, { profileIds });
+      log(`Set ${profileIds.length} profile(s) for project '${id}'.`);
+    });
+
+  return cmd;
+}
diff --git a/src/cli/src/index.ts b/src/cli/src/index.ts
index af3d6d5..16b1f01 100644
--- a/src/cli/src/index.ts
+++ b/src/cli/src/index.ts
@@ -8,6 +8,8 @@ import { createDescribeCommand } from './commands/describe.js';
 import { createInstanceCommands } from './commands/instances.js';
 import { createApplyCommand } from './commands/apply.js';
 import { createSetupCommand } from './commands/setup.js';
+import { createClaudeCommand } from './commands/claude.js';
+import { createProjectCommand } from './commands/project.js';
 import { ApiClient } from './api-client.js';
 import { loadConfig } from './config/index.js';
 
@@ -86,6 +88,16 @@ export function createProgram(): Command {
     log: (...args) => console.log(...args),
   }));
 
+  program.addCommand(createClaudeCommand({
+    client,
+    log: (...args) => console.log(...args),
+  }));
+
+  program.addCommand(createProjectCommand({
+    client,
+    log: (...args) => console.log(...args),
+  }));
+
   return program;
 }
 
diff --git a/src/cli/tests/commands/claude.test.ts b/src/cli/tests/commands/claude.test.ts
new file mode 100644
index 0000000..59b5a59
--- /dev/null
+++ b/src/cli/tests/commands/claude.test.ts
@@ -0,0 +1,158 @@
+import { describe, it, expect, vi, beforeEach } from 'vitest';
+import { writeFileSync, readFileSync, mkdtempSync, rmSync } from 'node:fs';
+import { join } from 'node:path';
+import { tmpdir } from 'node:os';
+import { createClaudeCommand } from '../../src/commands/claude.js';
+import type { ApiClient } from '../../src/api-client.js';
+
+function mockClient(): ApiClient {
+  return {
+    get: vi.fn(async () => ({
+      mcpServers: {
+        'slack--default': { command: 'npx', args: ['-y', '@anthropic/slack-mcp'], env: { WORKSPACE: 'test' } },
+        'github--default': { command: 'npx', args: ['-y', '@anthropic/github-mcp'] },
+      },
+    })),
+    post: vi.fn(async () => ({})),
+    put: vi.fn(async () => ({})),
+    delete: vi.fn(async () => {}),
+  } as unknown as ApiClient;
+}
+
+describe('claude command', () => {
+  let client: ReturnType<typeof mockClient>;
+  let output: string[];
+  let tmpDir: string;
+  const log = (...args: unknown[]) => output.push(args.map(String).join(' '));
+
+  beforeEach(() => {
+    client = mockClient();
+    output = [];
+    tmpDir = mkdtempSync(join(tmpdir(), 'mcpctl-claude-'));
+  });
+
+  describe('generate', () => {
+    it('generates .mcp.json from project config', async () => {
+      const outPath = join(tmpDir, '.mcp.json');
+      const cmd = createClaudeCommand({ client, log });
+      await cmd.parseAsync(['generate', 'proj-1', '-o', outPath], { from: 'user' });
+
+      expect(client.get).toHaveBeenCalledWith('/api/v1/projects/proj-1/mcp-config');
+      const written = JSON.parse(readFileSync(outPath, 'utf-8'));
+      expect(written.mcpServers['slack--default']).toBeDefined();
+      expect(output.join('\n')).toContain('2 server(s)');
+
+      rmSync(tmpDir, { recursive: true, force: true });
+    });
+
+    it('prints to stdout with --stdout', async () => {
+      const cmd = createClaudeCommand({ client, log });
+      await cmd.parseAsync(['generate', 'proj-1', '--stdout'], { from: 'user' });
+
+      expect(output[0]).toContain('mcpServers');
+      rmSync(tmpDir, { recursive: true, force: true });
+    });
+
+    it('merges with existing .mcp.json', async () => {
+      const outPath = join(tmpDir, '.mcp.json');
+      writeFileSync(outPath, JSON.stringify({
+        mcpServers: { 'existing--server': { command: 'echo', args: [] } },
+      }));
+
+      const cmd = createClaudeCommand({ client, log });
+      await cmd.parseAsync(['generate', 'proj-1', '-o', outPath, '--merge'], { from: 'user' });
+
+      const written = JSON.parse(readFileSync(outPath, 'utf-8'));
+      expect(written.mcpServers['existing--server']).toBeDefined();
+      expect(written.mcpServers['slack--default']).toBeDefined();
+      expect(output.join('\n')).toContain('3 server(s)');
+
+      rmSync(tmpDir, { recursive: true, force: true });
+    });
+  });
+
+  describe('show', () => {
+    it('shows servers in .mcp.json', () => {
+      const filePath = join(tmpDir, '.mcp.json');
+      writeFileSync(filePath, JSON.stringify({
+        mcpServers: {
+          'slack': { command: 'npx', args: ['-y', '@anthropic/slack-mcp'], env: { TOKEN: 'x' } },
+        },
+      }));
+
+      const cmd = createClaudeCommand({ client, log });
+      cmd.parseAsync(['show', '-p', filePath], { from: 'user' });
+
+      expect(output.join('\n')).toContain('slack');
+      expect(output.join('\n')).toContain('npx -y @anthropic/slack-mcp');
+      expect(output.join('\n')).toContain('TOKEN');
+
+      rmSync(tmpDir, { recursive: true, force: true });
+    });
+
+    it('handles missing file', () => {
+      const cmd = createClaudeCommand({ client, log });
+      cmd.parseAsync(['show', '-p', join(tmpDir, 'nonexistent.json')], { from: 'user' });
+
+      expect(output.join('\n')).toContain('No .mcp.json found');
+      rmSync(tmpDir, { recursive: true, force: true });
+    });
+  });
+
+  describe('add', () => {
+    it('adds a server entry', () => {
+      const filePath = join(tmpDir, '.mcp.json');
+      const cmd = createClaudeCommand({ client, log });
+      cmd.parseAsync(['add', 'my-server', '-c', 'npx', '-a', '-y', 'my-pkg', '-p', filePath], { from: 'user' });
+
+      const written = JSON.parse(readFileSync(filePath, 'utf-8'));
+      expect(written.mcpServers['my-server']).toEqual({
+        command: 'npx',
+        args: ['-y', 'my-pkg'],
+      });
+
+      rmSync(tmpDir, { recursive: true, force: true });
+    });
+
+    it('adds server with env vars', () => {
+      const filePath = join(tmpDir, '.mcp.json');
+      const cmd = createClaudeCommand({ client, log });
+      cmd.parseAsync(['add', 'my-server', '-c', 'node', '-e', 'KEY=val', 'SECRET=abc', '-p', filePath], { from: 'user' });
+
+      const written = JSON.parse(readFileSync(filePath, 'utf-8'));
+      expect(written.mcpServers['my-server'].env).toEqual({ KEY: 'val', SECRET: 'abc' });
+
+      rmSync(tmpDir, { recursive: true, force: true });
+    });
+  });
+
+  describe('remove', () => {
+    it('removes a server entry', () => {
+      const filePath = join(tmpDir, '.mcp.json');
+      writeFileSync(filePath, JSON.stringify({
+        mcpServers: { 'slack': { command: 'npx', args: [] }, 'github': { command: 'npx', args: [] } },
+      }));
+
+      const cmd = createClaudeCommand({ client, log });
+      cmd.parseAsync(['remove', 'slack', '-p', filePath], { from: 'user' });
+
+      const written = JSON.parse(readFileSync(filePath, 'utf-8'));
+      expect(written.mcpServers['slack']).toBeUndefined();
+      expect(written.mcpServers['github']).toBeDefined();
+      expect(output.join('\n')).toContain("Removed 'slack'");
+
+      rmSync(tmpDir, { recursive: true, force: true });
+    });
+
+    it('reports when server not found', () => {
+      const filePath = join(tmpDir, '.mcp.json');
+      writeFileSync(filePath, JSON.stringify({ mcpServers: {} }));
+
+      const cmd = createClaudeCommand({ client, log });
+      cmd.parseAsync(['remove', 'nonexistent', '-p', filePath], { from: 'user' });
+
+      expect(output.join('\n')).toContain('not found');
+      rmSync(tmpDir, { recursive: true, force: true });
+    });
+  });
+});
diff --git a/src/cli/tests/commands/project.test.ts b/src/cli/tests/commands/project.test.ts
new file mode 100644
index 0000000..bcc93c0
--- /dev/null
+++ b/src/cli/tests/commands/project.test.ts
@@ -0,0 +1,111 @@
+import { describe, it, expect, vi, beforeEach } from 'vitest';
+import { createProjectCommand } from '../../src/commands/project.js';
+import type { ApiClient } from '../../src/api-client.js';
+
+function mockClient(): ApiClient {
+  return {
+    get: vi.fn(async () => []),
+    post: vi.fn(async () => ({ id: 'proj-1', name: 'my-project' })),
+    put: vi.fn(async () => ({})),
+    delete: vi.fn(async () => {}),
+  } as unknown as ApiClient;
+}
+
+describe('project command', () => {
+  let client: ReturnType<typeof mockClient>;
+  let output: string[];
+  const log = (...args: unknown[]) => output.push(args.map(String).join(' '));
+
+  beforeEach(() => {
+    client = mockClient();
+    output = [];
+  });
+
+  describe('list', () => {
+    it('shows no projects message when empty', async () => {
+      const cmd = createProjectCommand({ client, log });
+      await cmd.parseAsync(['list'], { from: 'user' });
+      expect(output.join('\n')).toContain('No projects found');
+    });
+
+    it('shows project table', async () => {
+      vi.mocked(client.get).mockResolvedValue([
+        { id: 'proj-1', name: 'dev', description: 'Dev project', ownerId: 'user-1', createdAt: '2025-01-01' },
+      ]);
+      const cmd = createProjectCommand({ client, log });
+      await cmd.parseAsync(['list'], { from: 'user' });
+      expect(output.join('\n')).toContain('proj-1');
+      expect(output.join('\n')).toContain('dev');
+    });
+
+    it('outputs json', async () => {
+      vi.mocked(client.get).mockResolvedValue([{ id: 'proj-1', name: 'dev' }]);
+      const cmd = createProjectCommand({ client, log });
+      await cmd.parseAsync(['list', '-o', 'json'], { from: 'user' });
+      expect(output[0]).toContain('"id"');
+    });
+  });
+
+  describe('create', () => {
+    it('creates a project', async () => {
+      const cmd = createProjectCommand({ client, log });
+      await cmd.parseAsync(['create', 'my-project', '-d', 'A test project'], { from: 'user' });
+      expect(client.post).toHaveBeenCalledWith('/api/v1/projects', {
+        name: 'my-project',
+        description: 'A test project',
+      });
+      expect(output.join('\n')).toContain("Project 'my-project' created");
+    });
+  });
+
+  describe('delete', () => {
+    it('deletes a project', async () => {
+      const cmd = createProjectCommand({ client, log });
+      await cmd.parseAsync(['delete', 'proj-1'], { from: 'user' });
+      expect(client.delete).toHaveBeenCalledWith('/api/v1/projects/proj-1');
+      expect(output.join('\n')).toContain('deleted');
+    });
+  });
+
+  describe('show', () => {
+    it('shows project details', async () => {
+      vi.mocked(client.get).mockImplementation(async (url: string) => {
+        if (url.endsWith('/profiles')) return [];
+        return { id: 'proj-1', name: 'dev', description: 'Dev project', ownerId: 'user-1', createdAt: '2025-01-01' };
+      });
+      const cmd = createProjectCommand({ client, log });
+      await cmd.parseAsync(['show', 'proj-1'], { from: 'user' });
+      expect(output.join('\n')).toContain('Name: dev');
+      expect(output.join('\n')).toContain('ID: proj-1');
+    });
+  });
+
+  describe('profiles', () => {
+    it('lists profiles for a project', async () => {
+      vi.mocked(client.get).mockResolvedValue([
+        { id: 'prof-1', name: 'default', serverId: 'srv-1' },
+      ]);
+      const cmd = createProjectCommand({ client, log });
+      await cmd.parseAsync(['profiles', 'proj-1'], { from: 'user' });
+      expect(client.get).toHaveBeenCalledWith('/api/v1/projects/proj-1/profiles');
+      expect(output.join('\n')).toContain('default');
+    });
+
+    it('shows empty message when no profiles', async () => {
+      const cmd = createProjectCommand({ client, log });
+      await cmd.parseAsync(['profiles', 'proj-1'], { from: 'user' });
+      expect(output.join('\n')).toContain('No profiles assigned');
+    });
+  });
+
+  describe('set-profiles', () => {
+    it('sets profiles for a project', async () => {
+      const cmd = createProjectCommand({ client, log });
+      await cmd.parseAsync(['set-profiles', 'proj-1', 'prof-1', 'prof-2'], { from: 'user' });
+      expect(client.put).toHaveBeenCalledWith('/api/v1/projects/proj-1/profiles', {
+        profileIds: ['prof-1', 'prof-2'],
+      });
+      expect(output.join('\n')).toContain('2 profile(s)');
+    });
+  });
+});