diff --git a/test/test-installation-components.js b/test/test-installation-components.js
index d51ccbd8a..23c8f6382 100644
--- a/test/test-installation-components.js
+++ b/test/test-installation-components.js
@@ -1134,6 +1134,87 @@ async function runTests() {
 
   console.log('');
 
+  // ============================================================
+  // Suite 22: KiloCoder Native Skills
+  // ============================================================
+  console.log(`${colors.yellow}Test Suite 22: KiloCoder Native Skills${colors.reset}\n`);
+
+  try {
+    clearCache();
+    const platformCodes22 = await loadPlatformCodes();
+    const kiloInstaller = platformCodes22.platforms.kilo?.installer;
+
+    assert(kiloInstaller?.target_dir === '.kilocode/skills', 'KiloCoder target_dir uses native skills path');
+
+    assert(kiloInstaller?.skill_format === true, 'KiloCoder installer enables native skill output');
+
+    assert(
+      Array.isArray(kiloInstaller?.legacy_targets) && kiloInstaller.legacy_targets.includes('.kilocode/workflows'),
+      'KiloCoder installer cleans legacy workflows output',
+    );
+
+    // Fresh install test
+    const tempProjectDir22 = await fs.mkdtemp(path.join(os.tmpdir(), 'bmad-kilo-test-'));
+    const installedBmadDir22 = await createTestBmadFixture();
+    const legacyDir22 = path.join(tempProjectDir22, '.kilocode', 'workflows');
+    await fs.ensureDir(legacyDir22);
+    await fs.writeFile(path.join(legacyDir22, 'bmad-legacy.md'), 'legacy\n');
+
+    // Create a .kilocodemodes file with BMAD modes and a user mode
+    const kiloModesPath22 = path.join(tempProjectDir22, '.kilocodemodes');
+    const yaml22 = require('yaml');
+    const kiloModesContent = yaml22.stringify({
+      customModes: [
+        { slug: 'bmad-bmm-architect', name: 'BMAD Architect', roleDefinition: 'test' },
+        { slug: 'bmad-core-master', name: 'BMAD Master', roleDefinition: 'test' },
+        { slug: 'user-custom-mode', name: 'My Custom Mode', roleDefinition: 'user mode' },
+      ],
+    });
+    await fs.writeFile(kiloModesPath22, kiloModesContent);
+
+    const ideManager22 = new IdeManager();
+    await ideManager22.ensureInitialized();
+    const result22 = await ideManager22.setup('kilo', tempProjectDir22, installedBmadDir22, {
+      silent: true,
+      selectedModules: ['bmm'],
+    });
+
+    assert(result22.success === true, 'KiloCoder setup succeeds against temp project');
+
+    const skillFile22 = path.join(tempProjectDir22, '.kilocode', 'skills', 'bmad-master', 'SKILL.md');
+    assert(await fs.pathExists(skillFile22), 'KiloCoder install writes SKILL.md directory output');
+
+    const skillContent22 = await fs.readFile(skillFile22, 'utf8');
+    const nameMatch22 = skillContent22.match(/^name:\s*(.+)$/m);
+    assert(nameMatch22 && nameMatch22[1].trim() === 'bmad-master', 'KiloCoder skill name frontmatter matches directory name exactly');
+
+    assert(!(await fs.pathExists(path.join(tempProjectDir22, '.kilocode', 'workflows'))), 'KiloCoder setup removes legacy workflows dir');
+
+    // Verify .kilocodemodes cleanup: BMAD modes removed, user mode preserved
+    const cleanedModes22 = yaml22.parse(await fs.readFile(kiloModesPath22, 'utf8'));
+    assert(
+      Array.isArray(cleanedModes22.customModes) && cleanedModes22.customModes.length === 1,
+      'KiloCoder cleanup removes BMAD modes from .kilocodemodes',
+    );
+    assert(cleanedModes22.customModes[0].slug === 'user-custom-mode', 'KiloCoder cleanup preserves non-BMAD modes in .kilocodemodes');
+
+    // Reinstall test
+    const result22b = await ideManager22.setup('kilo', tempProjectDir22, installedBmadDir22, {
+      silent: true,
+      selectedModules: ['bmm'],
+    });
+
+    assert(result22b.success === true, 'KiloCoder reinstall/upgrade succeeds over existing skills');
+    assert(await fs.pathExists(skillFile22), 'KiloCoder reinstall preserves SKILL.md output');
+
+    await fs.remove(tempProjectDir22);
+    await fs.remove(installedBmadDir22);
+  } catch (error) {
+    assert(false, 'KiloCoder native skills migration test succeeds', error.message);
+  }
+
+  console.log('');
+
   // ============================================================
   // Summary
   // ============================================================
diff --git a/tools/cli/installers/lib/ide/_config-driven.js b/tools/cli/installers/lib/ide/_config-driven.js
index 030b85e19..3ade16b47 100644
--- a/tools/cli/installers/lib/ide/_config-driven.js
+++ b/tools/cli/installers/lib/ide/_config-driven.js
@@ -660,6 +660,11 @@ LOAD and execute from: {project-root}/{{bmadFolderName}}/{{path}}
       await this.cleanupCopilotInstructions(projectDir, options);
     }
 
+    // Strip BMAD modes from .kilocodemodes if present
+    if (this.name === 'kilo') {
+      await this.cleanupKiloModes(projectDir, options);
+    }
+
     // Clean all target directories
     if (this.installerConfig?.targets) {
       const parentDirs = new Set();
@@ -807,6 +812,42 @@ LOAD and execute from: {project-root}/{{bmadFolderName}}/{{path}}
     if (!options.silent) await prompts.log.message('  Cleaned BMAD markers from copilot-instructions.md');
   }
 
+  /**
+   * Strip BMAD-owned modes from .kilocodemodes.
+   * The old custom kilo.js installer added modes with slug starting with 'bmad-'.
+   * Parses YAML, filters out BMAD modes, rewrites. Leaves file as-is on parse failure.
+   */
+  async cleanupKiloModes(projectDir, options = {}) {
+    const kiloModesPath = path.join(projectDir, '.kilocodemodes');
+
+    if (!(await fs.pathExists(kiloModesPath))) return;
+
+    const content = await fs.readFile(kiloModesPath, 'utf8');
+
+    let config;
+    try {
+      config = yaml.parse(content) || {};
+    } catch {
+      if (!options.silent) await prompts.log.warn('  Warning: Could not parse .kilocodemodes for cleanup');
+      return;
+    }
+
+    if (!Array.isArray(config.customModes)) return;
+
+    const originalCount = config.customModes.length;
+    config.customModes = config.customModes.filter((mode) => mode && (!mode.slug || !mode.slug.startsWith('bmad-')));
+    const removedCount = originalCount - config.customModes.length;
+
+    if (removedCount > 0) {
+      try {
+        await fs.writeFile(kiloModesPath, yaml.stringify(config, { lineWidth: 0 }));
+        if (!options.silent) await prompts.log.message(`  Removed ${removedCount} BMAD modes from .kilocodemodes`);
+      } catch {
+        if (!options.silent) await prompts.log.warn('  Warning: Could not write .kilocodemodes during cleanup');
+      }
+    }
+  }
+
   /**
    * Check ancestor directories for existing BMAD files in the same target_dir.
    * IDEs like Claude Code inherit commands from parent directories, so an existing
diff --git a/tools/cli/installers/lib/ide/kilo.js b/tools/cli/installers/lib/ide/kilo.js
deleted file mode 100644
index 2e5734391..000000000
--- a/tools/cli/installers/lib/ide/kilo.js
+++ /dev/null
@@ -1,269 +0,0 @@
-const path = require('node:path');
-const { BaseIdeSetup } = require('./_base-ide');
-const yaml = require('yaml');
-const prompts = require('../../../lib/prompts');
-const { AgentCommandGenerator } = require('./shared/agent-command-generator');
-const { WorkflowCommandGenerator } = require('./shared/workflow-command-generator');
-const { TaskToolCommandGenerator } = require('./shared/task-tool-command-generator');
-
-/**
- * KiloCode IDE setup handler
- * Creates custom modes in .kilocodemodes file (similar to Roo)
- */
-class KiloSetup extends BaseIdeSetup {
-  constructor() {
-    super('kilo', 'Kilo Code');
-    this.configFile = '.kilocodemodes';
-  }
-
-  /**
-   * Setup KiloCode IDE configuration
-   * @param {string} projectDir - Project directory
-   * @param {string} bmadDir - BMAD installation directory
-   * @param {Object} options - Setup options
-   */
-  async setup(projectDir, bmadDir, options = {}) {
-    if (!options.silent) await prompts.log.info(`Setting up ${this.name}...`);
-
-    // Clean up any old BMAD installation first
-    await this.cleanup(projectDir, options);
-
-    // Load existing config (may contain non-BMAD modes and other settings)
-    const kiloModesPath = path.join(projectDir, this.configFile);
-    let config = {};
-
-    if (await this.pathExists(kiloModesPath)) {
-      const existingContent = await this.readFile(kiloModesPath);
-      try {
-        config = yaml.parse(existingContent) || {};
-      } catch {
-        // If parsing fails, start fresh but warn user
-        await prompts.log.warn('Warning: Could not parse existing .kilocodemodes, starting fresh');
-        config = {};
-      }
-    }
-
-    // Ensure customModes array exists
-    if (!Array.isArray(config.customModes)) {
-      config.customModes = [];
-    }
-
-    // Generate agent launchers
-    const agentGen = new AgentCommandGenerator(this.bmadFolderName);
-    const { artifacts: agentArtifacts } = await agentGen.collectAgentArtifacts(bmadDir, options.selectedModules || []);
-
-    // Create mode objects and add to config
-    let addedCount = 0;
-
-    for (const artifact of agentArtifacts) {
-      const modeObject = await this.createModeObject(artifact, projectDir);
-      config.customModes.push(modeObject);
-      addedCount++;
-    }
-
-    // Write .kilocodemodes file with proper YAML structure
-    const finalContent = yaml.stringify(config, { lineWidth: 0 });
-    await this.writeFile(kiloModesPath, finalContent);
-
-    // Generate workflow commands
-    const workflowGenerator = new WorkflowCommandGenerator(this.bmadFolderName);
-    const { artifacts: workflowArtifacts } = await workflowGenerator.collectWorkflowArtifacts(bmadDir);
-
-    // Write to .kilocode/workflows/ directory
-    const workflowsDir = path.join(projectDir, '.kilocode', 'workflows');
-    await this.ensureDir(workflowsDir);
-
-    // Clear old BMAD workflows before writing new ones
-    await this.clearBmadWorkflows(workflowsDir);
-
-    // Write workflow files
-    const workflowCount = await workflowGenerator.writeDashArtifacts(workflowsDir, workflowArtifacts);
-
-    // Generate task and tool commands
-    const taskToolGen = new TaskToolCommandGenerator(this.bmadFolderName);
-    const { artifacts: taskToolArtifacts, counts: taskToolCounts } = await taskToolGen.collectTaskToolArtifacts(bmadDir);
-
-    // Write task/tool files to workflows directory (same location as workflows)
-    await taskToolGen.writeDashArtifacts(workflowsDir, taskToolArtifacts);
-    const taskCount = taskToolCounts.tasks || 0;
-    const toolCount = taskToolCounts.tools || 0;
-
-    if (!options.silent) {
-      await prompts.log.success(
-        `${this.name} configured: ${addedCount} modes, ${workflowCount} workflows, ${taskCount} tasks, ${toolCount} tools → ${this.configFile}`,
-      );
-    }
-
-    return {
-      success: true,
-      modes: addedCount,
-      workflows: workflowCount,
-      tasks: taskCount,
-      tools: toolCount,
-    };
-  }
-
-  /**
-   * Create a mode object for an agent
-   * @param {Object} artifact - Agent artifact
-   * @param {string} projectDir - Project directory
-   * @returns {Object} Mode object for YAML serialization
-   */
-  async createModeObject(artifact, projectDir) {
-    // Extract metadata from launcher content
-    const titleMatch = artifact.content.match(/title="([^"]+)"/);
-    const title = titleMatch ? titleMatch[1] : this.formatTitle(artifact.name);
-
-    const iconMatch = artifact.content.match(/icon="([^"]+)"/);
-    const icon = iconMatch ? iconMatch[1] : '🤖';
-
-    const whenToUseMatch = artifact.content.match(/whenToUse="([^"]+)"/);
-    const whenToUse = whenToUseMatch ? whenToUseMatch[1] : `Use for ${title} tasks`;
-
-    // Get the activation header from central template (trim to avoid YAML formatting issues)
-    const activationHeader = (await this.getAgentCommandHeader()).trim();
-
-    const roleDefinitionMatch = artifact.content.match(/roleDefinition="([^"]+)"/);
-    const roleDefinition = roleDefinitionMatch
-      ? roleDefinitionMatch[1]
-      : `You are a ${title} specializing in ${title.toLowerCase()} tasks.`;
-
-    // Get relative path
-    const relativePath = path.relative(projectDir, artifact.sourcePath).replaceAll('\\', '/');
-
-    // Build mode object (KiloCode uses same schema as Roo)
-    return {
-      slug: `bmad-${artifact.module}-${artifact.name}`,
-      name: `${icon} ${title}`,
-      roleDefinition: roleDefinition,
-      whenToUse: whenToUse,
-      customInstructions: `${activationHeader} Read the full YAML from ${relativePath} start activation to alter your state of being follow startup section instructions stay in this being until told to exit this mode\n`,
-      groups: ['read', 'edit', 'browser', 'command', 'mcp'],
-    };
-  }
-
-  /**
-   * Format name as title
-   */
-  formatTitle(name) {
-    return name
-      .split('-')
-      .map((word) => word.charAt(0).toUpperCase() + word.slice(1))
-      .join(' ');
-  }
-
-  /**
-   * Clear old BMAD workflow files from workflows directory
-   * @param {string} workflowsDir - Workflows directory path
-   */
-  async clearBmadWorkflows(workflowsDir) {
-    const fs = require('fs-extra');
-    if (!(await fs.pathExists(workflowsDir))) return;
-
-    const entries = await fs.readdir(workflowsDir);
-    for (const entry of entries) {
-      if (entry.startsWith('bmad-') && entry.endsWith('.md')) {
-        await fs.remove(path.join(workflowsDir, entry));
-      }
-    }
-  }
-
-  /**
-   * Cleanup KiloCode configuration
-   */
-  async cleanup(projectDir, options = {}) {
-    const fs = require('fs-extra');
-    const kiloModesPath = path.join(projectDir, this.configFile);
-
-    if (await fs.pathExists(kiloModesPath)) {
-      const content = await fs.readFile(kiloModesPath, 'utf8');
-
-      try {
-        const config = yaml.parse(content) || {};
-
-        if (Array.isArray(config.customModes)) {
-          const originalCount = config.customModes.length;
-          // Remove BMAD modes only (keep non-BMAD modes)
-          config.customModes = config.customModes.filter((mode) => !mode.slug || !mode.slug.startsWith('bmad-'));
-          const removedCount = originalCount - config.customModes.length;
-
-          if (removedCount > 0) {
-            await fs.writeFile(kiloModesPath, yaml.stringify(config, { lineWidth: 0 }));
-            if (!options.silent) await prompts.log.message(`Removed ${removedCount} BMAD modes from .kilocodemodes`);
-          }
-        }
-      } catch {
-        // If parsing fails, leave file as-is
-        if (!options.silent) await prompts.log.warn('Warning: Could not parse .kilocodemodes for cleanup');
-      }
-    }
-
-    // Clean up workflow files
-    const workflowsDir = path.join(projectDir, '.kilocode', 'workflows');
-    await this.clearBmadWorkflows(workflowsDir);
-  }
-
-  /**
-   * Install a custom agent launcher for Kilo
-   * @param {string} projectDir - Project directory
-   * @param {string} agentName - Agent name (e.g., "fred-commit-poet")
-   * @param {string} agentPath - Path to compiled agent (relative to project root)
-   * @param {Object} metadata - Agent metadata
-   * @returns {Object} Installation result
-   */
-  async installCustomAgentLauncher(projectDir, agentName, agentPath, metadata) {
-    const kilocodemodesPath = path.join(projectDir, this.configFile);
-    let config = {};
-
-    // Read existing .kilocodemodes file
-    if (await this.pathExists(kilocodemodesPath)) {
-      const existingContent = await this.readFile(kilocodemodesPath);
-      try {
-        config = yaml.parse(existingContent) || {};
-      } catch {
-        config = {};
-      }
-    }
-
-    // Ensure customModes array exists
-    if (!Array.isArray(config.customModes)) {
-      config.customModes = [];
-    }
-
-    // Create custom agent mode object
-    const slug = `bmad-custom-${agentName.toLowerCase()}`;
-
-    // Check if mode already exists
-    if (config.customModes.some((mode) => mode.slug === slug)) {
-      return {
-        ide: 'kilo',
-        path: this.configFile,
-        command: agentName,
-        type: 'custom-agent-launcher',
-        alreadyExists: true,
-      };
-    }
-
-    // Add custom mode object
-    config.customModes.push({
-      slug: slug,
-      name: `BMAD Custom: ${agentName}`,
-      description: `Custom BMAD agent: ${agentName}\n\n**⚠️ IMPORTANT**: Run @${agentPath} first to load the complete agent!\n\nThis is a launcher for the custom BMAD agent "${agentName}". The agent will follow the persona and instructions from the main agent file.\n`,
-      prompt: `@${agentPath}\n`,
-      always: false,
-      permissions: 'all',
-    });
-
-    // Write .kilocodemodes file with proper YAML structure
-    await this.writeFile(kilocodemodesPath, yaml.stringify(config, { lineWidth: 0 }));
-
-    return {
-      ide: 'kilo',
-      path: this.configFile,
-      command: slug,
-      type: 'custom-agent-launcher',
-    };
-  }
-}
-
-module.exports = { KiloSetup };
diff --git a/tools/cli/installers/lib/ide/manager.js b/tools/cli/installers/lib/ide/manager.js
index 0ed8f8006..908a094a3 100644
--- a/tools/cli/installers/lib/ide/manager.js
+++ b/tools/cli/installers/lib/ide/manager.js
@@ -8,7 +8,7 @@ const prompts = require('../../../lib/prompts');
  * Dynamically discovers and loads IDE handlers
  *
  * Loading strategy:
- * 1. Custom installer files (kilo.js, rovodev.js) - for platforms with unique installation logic
+ * 1. Custom installer files (rovodev.js) - for platforms with unique installation logic
  * 2. Config-driven handlers (from platform-codes.yaml) - for standard IDE installation patterns
  */
 class IdeManager {
@@ -58,11 +58,11 @@ class IdeManager {
   /**
    * Load custom installer files (unique installation logic)
    * These files have special installation patterns that don't fit the config-driven model
-   * Note: codex and github-copilot were migrated to config-driven (platform-codes.yaml)
+   * Note: codex, github-copilot, and kilo were migrated to config-driven (platform-codes.yaml)
    */
   async loadCustomInstallerFiles() {
     const ideDir = __dirname;
-    const customFiles = ['kilo.js', 'rovodev.js'];
+    const customFiles = ['rovodev.js'];
 
     for (const file of customFiles) {
       const filePath = path.join(ideDir, file);
@@ -190,14 +190,6 @@ class IdeManager {
         if (r.tasks > 0) parts.push(`${r.tasks} tasks`);
         if (r.tools > 0) parts.push(`${r.tools} tools`);
         detail = parts.join(', ');
-      } else if (handlerResult && handlerResult.modes !== undefined) {
-        // Kilo handler returns { success, modes, workflows, tasks, tools }
-        const parts = [];
-        if (handlerResult.modes > 0) parts.push(`${handlerResult.modes} modes`);
-        if (handlerResult.workflows > 0) parts.push(`${handlerResult.workflows} workflows`);
-        if (handlerResult.tasks > 0) parts.push(`${handlerResult.tasks} tasks`);
-        if (handlerResult.tools > 0) parts.push(`${handlerResult.tools} tools`);
-        detail = parts.join(', ');
       }
       // Propagate handler's success status (default true for backward compat)
       const success = handlerResult?.success !== false;
diff --git a/tools/cli/installers/lib/ide/platform-codes.yaml b/tools/cli/installers/lib/ide/platform-codes.yaml
index e3b6f044f..37497c86b 100644
--- a/tools/cli/installers/lib/ide/platform-codes.yaml
+++ b/tools/cli/installers/lib/ide/platform-codes.yaml
@@ -150,7 +150,12 @@ platforms:
     preferred: false
     category: ide
     description: "AI coding platform"
-    # No installer config - uses custom kilo.js (creates .kilocodemodes file)
+    installer:
+      legacy_targets:
+        - .kilocode/workflows
+      target_dir: .kilocode/skills
+      template_type: default
+      skill_format: true
 
   kiro:
     name: "Kiro"
diff --git a/tools/docs/native-skills-migration-checklist.md b/tools/docs/native-skills-migration-checklist.md
index 973e94282..614871f99 100644
--- a/tools/docs/native-skills-migration-checklist.md
+++ b/tools/docs/native-skills-migration-checklist.md
@@ -211,14 +211,14 @@ Support assumption: full Agent Skills support. BMAD currently uses a custom inst
 
 **Install:** VS Code extension `kilocode.kilo-code` — search "Kilo Code" in Extensions or `code --install-extension kilocode.kilo-code`
 
-- [ ] Confirm KiloCoder native skills path and whether `.kilocodemodes` should be removed entirely or retained temporarily for compatibility
-- [ ] Design the migration away from modes plus workflow markdown
-- [ ] Implement native skills output
-- [ ] Add legacy cleanup for `.kilocode/workflows` and BMAD-owned entries in `.kilocodemodes`
-- [ ] Test fresh install
-- [ ] Test reinstall/upgrade from legacy custom installer output
-- [ ] Confirm ancestor conflict protection where applicable
-- [ ] Implement/extend automated tests
+- [x] Confirm KiloCoder native skills path is `.kilocode/skills/{skill-name}/SKILL.md` (Kilo forked from Roo Code which uses `.roo/skills/`)
+- [x] Design the migration away from modes plus workflow markdown — replaced 269-line custom kilo.js with config-driven installer entry in platform-codes.yaml
+- [x] Implement native skills output — target_dir `.kilocode/skills`, skill_format true, template_type default
+- [x] Add legacy cleanup for `.kilocode/workflows` (via legacy_targets) and BMAD-owned entries in `.kilocodemodes` (via `cleanupKiloModes()` in `_config-driven.js`, same pattern as `copilot-instructions.md` cleanup)
+- [x] Test fresh install — skills written to `.kilocode/skills/bmad-master/SKILL.md` with correct frontmatter
+- [x] Test reinstall/upgrade from legacy custom installer output — legacy workflows removed, skills installed
+- [x] Confirm no ancestor conflict protection is needed — Kilo Code (like Cline) only scans workspace-local `.kilocode/skills/`, no ancestor directory inheritance
+- [x] Implement/extend automated tests — 11 assertions in test suite 22 (config, fresh install, legacy cleanup, .kilocodemodes cleanup, reinstall)
 - [ ] Commit
 
 ## Summary Gates