diff --git a/test/test-installation-components.js b/test/test-installation-components.js
index 4e5fa7282..0b792cef7 100644
--- a/test/test-installation-components.js
+++ b/test/test-installation-components.js
@@ -126,6 +126,53 @@ async function createSkillCollisionFixture() {
   return { root: fixtureRoot, bmadDir: fixtureDir };
 }
 
+async function createCustomModuleManifestFixture() {
+  const fixtureRoot = await fs.mkdtemp(path.join(os.tmpdir(), 'bmad-custom-manifest-'));
+  const bmadDir = path.join(fixtureRoot, '_bmad');
+  const configDir = path.join(bmadDir, '_config');
+  await fs.ensureDir(configDir);
+
+  const minimalAgent = '<agent name="Test" title="T"><persona>p</persona></agent>';
+  await fs.ensureDir(path.join(bmadDir, 'core', 'agents'));
+  await fs.writeFile(path.join(bmadDir, 'core', 'agents', 'test.md'), minimalAgent);
+  await fs.ensureDir(path.join(bmadDir, 'test-module', 'agents'));
+  await fs.writeFile(path.join(bmadDir, 'test-module', 'agents', 'test.md'), minimalAgent);
+
+  await fs.writeFile(
+    path.join(configDir, 'manifest.yaml'),
+    [
+      'installation:',
+      '  version: 6.2.2',
+      '  installDate: 2026-03-30T00:00:00.000Z',
+      '  lastUpdated: 2026-03-30T00:00:00.000Z',
+      'modules:',
+      '  - name: core',
+      '    version: 6.2.2',
+      '    installDate: 2026-03-30T00:00:00.000Z',
+      '    lastUpdated: 2026-03-30T00:00:00.000Z',
+      '    source: built-in',
+      '    npmPackage: null',
+      '    repoUrl: null',
+      '  - name: test-module',
+      '    version: null',
+      '    installDate: 2026-03-30T00:00:00.000Z',
+      '    lastUpdated: 2026-03-30T00:00:00.000Z',
+      '    source: custom',
+      '    npmPackage: null',
+      '    repoUrl: null',
+      'customModules:',
+      '  - id: test-module',
+      '    name: "Test Module"',
+      '    sourcePath: "/tmp/test-module-source"',
+      'ides:',
+      '  - codex',
+      '',
+    ].join('\n'),
+  );
+
+  return { root: fixtureRoot, bmadDir, manifestPath: path.join(configDir, 'manifest.yaml') };
+}
+
 /**
  * Test Suite
  */
@@ -1713,6 +1760,35 @@ async function runTests() {
 
   console.log('');
 
+  // ============================================================
+  // Suite 33: Main manifest preserves customModules
+  // ============================================================
+  console.log(`${colors.yellow}Test Suite 33: Preserve customModules in main manifest${colors.reset}\n`);
+
+  let customManifestFixture = null;
+  try {
+    customManifestFixture = await createCustomModuleManifestFixture();
+    const generator33 = new ManifestGenerator();
+    await generator33.generateManifests(customManifestFixture.bmadDir, ['core', 'test-module'], [], { ides: ['codex'] });
+
+    const yaml = require('yaml');
+    const updatedManifest = yaml.parse(await fs.readFile(customManifestFixture.manifestPath, 'utf8'));
+    const customModule = updatedManifest.customModules?.find((entry) => entry.id === 'test-module');
+
+    assert(Array.isArray(updatedManifest.customModules), 'Main manifest keeps customModules array');
+    assert(customModule !== undefined, 'Main manifest preserves existing custom module entry');
+    assert(
+      customModule && customModule.sourcePath === '/tmp/test-module-source',
+      'Main manifest preserves custom module sourcePath',
+    );
+  } catch (error) {
+    assert(false, 'Main manifest preserves customModules test succeeds', error.message);
+  } finally {
+    if (customManifestFixture?.root) await fs.remove(customManifestFixture.root).catch(() => { });
+  }
+
+  console.log('');
+
   // ============================================================
   // Summary
   // ============================================================
diff --git a/tools/installer/core/installer.js b/tools/installer/core/installer.js
index 111c88b54..7beeb847d 100644
--- a/tools/installer/core/installer.js
+++ b/tools/installer/core/installer.js
@@ -1144,8 +1144,35 @@ class Installer {
     const configuredIdes = existingInstall.ides;
     const projectRoot = path.dirname(bmadDir);
 
-    // Get custom module sources: first from --custom-content (re-cache from source), then from cache
+    // Get custom module sources: first from manifest, then from --custom-content, then from cache
     const customModuleSources = new Map();
+    if (existingInstall.customModules) {
+      for (const customModule of existingInstall.customModules) {
+        if (!customModule?.id) continue;
+
+        let sourcePath = customModule.sourcePath;
+        if (sourcePath && sourcePath.startsWith('_config')) {
+          sourcePath = path.join(bmadDir, sourcePath);
+        } else if (!sourcePath && customModule.relativePath) {
+          sourcePath = path.resolve(projectRoot, customModule.relativePath);
+        } else if (sourcePath && !path.isAbsolute(sourcePath)) {
+          sourcePath = path.resolve(sourcePath);
+        }
+
+        if (!sourcePath || !(await fs.pathExists(sourcePath))) {
+          continue;
+        }
+
+        customModuleSources.set(customModule.id, {
+          id: customModule.id,
+          name: customModule.name || customModule.id,
+          sourcePath,
+          relativePath: customModule.relativePath,
+          cached: false,
+        });
+      }
+    }
+
     if (config.customContent?.sources?.length > 0) {
       for (const source of config.customContent.sources) {
         if (source.id && source.path && (await fs.pathExists(source.path))) {
diff --git a/tools/installer/core/manifest-generator.js b/tools/installer/core/manifest-generator.js
index 65e0f4ed3..f96081494 100644
--- a/tools/installer/core/manifest-generator.js
+++ b/tools/installer/core/manifest-generator.js
@@ -381,6 +381,7 @@ class ManifestGenerator {
     // Read existing manifest to preserve install date
     let existingInstallDate = null;
     const existingModulesMap = new Map();
+    let existingCustomModules = [];
 
     if (await fs.pathExists(manifestPath)) {
       try {
@@ -402,6 +403,10 @@ class ManifestGenerator {
             }
           }
         }
+
+        if (existingManifest.customModules && Array.isArray(existingManifest.customModules)) {
+          existingCustomModules = existingManifest.customModules;
+        }
       } catch {
         // If we can't read existing manifest, continue with defaults
       }
@@ -437,6 +442,7 @@ class ManifestGenerator {
         lastUpdated: new Date().toISOString(),
       },
       modules: updatedModules,
+      customModules: existingCustomModules,
       ides: this.selectedIdes,
     };