diff --git a/src/utility/agent-components/agent.customize.template.yaml b/src/utility/agent-components/agent.customize.template.yaml
index 3fb4785f..b8cc648b 100644
--- a/src/utility/agent-components/agent.customize.template.yaml
+++ b/src/utility/agent-components/agent.customize.template.yaml
@@ -1,6 +1,5 @@
 # Agent Customization
 # Customize any section below - all are optional
-# After editing: npx bmad-method build <agent-name>
 
 # Override agent name
 agent:
diff --git a/tools/cli/installers/lib/core/installer.js b/tools/cli/installers/lib/core/installer.js
index 77ec343c..b749e0d4 100644
--- a/tools/cli/installers/lib/core/installer.js
+++ b/tools/cli/installers/lib/core/installer.js
@@ -2798,11 +2798,28 @@ If AgentVibes party mode is enabled, immediately trigger TTS with agent's voice:
             const relativePath = path.relative(bmadDir, fullPath);
             const fileName = path.basename(fullPath);
 
-            // Skip _cfg directory EXCEPT for agent customizations
-            if (
-              (relativePath.startsWith('_cfg/') || relativePath.startsWith('_cfg\\')) && // Allow .customize.yaml files in _cfg/agents/
-              !(relativePath.includes('/agents/') && fileName.endsWith('.customize.yaml'))
-            ) {
+            // Skip _cfg directory EXCEPT for modified agent customizations
+            if (relativePath.startsWith('_cfg/') || relativePath.startsWith('_cfg\\')) {
+              // Special handling for .customize.yaml files - only preserve if modified
+              if (relativePath.includes('/agents/') && fileName.endsWith('.customize.yaml')) {
+                // Check if the customization file has been modified from manifest
+                const manifestPath = path.join(bmadDir, '_cfg', 'manifest.yaml');
+                if (await fs.pathExists(manifestPath)) {
+                  const crypto = require('node:crypto');
+                  const currentContent = await fs.readFile(fullPath, 'utf8');
+                  const currentHash = crypto.createHash('sha256').update(currentContent).digest('hex');
+
+                  const yaml = require('yaml');
+                  const manifestContent = await fs.readFile(manifestPath, 'utf8');
+                  const manifestData = yaml.parse(manifestContent);
+                  const originalHash = manifestData.agentCustomizations?.[relativePath];
+
+                  // Only add to customFiles if hash differs (user modified)
+                  if (originalHash && currentHash !== originalHash) {
+                    customFiles.push(fullPath);
+                  }
+                }
+              }
               continue;
             }
 
@@ -2814,7 +2831,11 @@ If AgentVibes party mode is enabled, immediately trigger TTS with agent's voice:
 
             if (!fileInfo) {
               // File not in manifest = custom file
-              customFiles.push(fullPath);
+              // EXCEPT: Agent .md files in module folders are generated files, not custom
+              // Only treat .md files under _cfg/agents/ as custom
+              if (!(fileName.endsWith('.md') && relativePath.includes('/agents/') && !relativePath.startsWith('_cfg/'))) {
+                customFiles.push(fullPath);
+              }
             } else if (manifestHasHashes && fileInfo.hash) {
               // File in manifest with hash - check if it was modified
               const currentHash = await this.manifest.calculateFileHash(fullPath);
diff --git a/tools/cli/installers/lib/modules/manager.js b/tools/cli/installers/lib/modules/manager.js
index 73e9b6ab..55cc6039 100644
--- a/tools/cli/installers/lib/modules/manager.js
+++ b/tools/cli/installers/lib/modules/manager.js
@@ -820,6 +820,32 @@ class ModuleManager {
           if (await fs.pathExists(genericTemplatePath)) {
             await this.copyFileWithPlaceholderReplacement(genericTemplatePath, customizePath);
             console.log(chalk.dim(`  Created customize: ${moduleName}-${agentName}.customize.yaml`));
+
+            // Store original hash for modification detection
+            const crypto = require('node:crypto');
+            const customizeContent = await fs.readFile(customizePath, 'utf8');
+            const originalHash = crypto.createHash('sha256').update(customizeContent).digest('hex');
+
+            // Store in main manifest
+            const manifestPath = path.join(bmadDir, '_cfg', 'manifest.yaml');
+            let manifestData = {};
+            if (await fs.pathExists(manifestPath)) {
+              const manifestContent = await fs.readFile(manifestPath, 'utf8');
+              const yaml = require('yaml');
+              manifestData = yaml.parse(manifestContent);
+            }
+            if (!manifestData.agentCustomizations) {
+              manifestData.agentCustomizations = {};
+            }
+            manifestData.agentCustomizations[path.relative(bmadDir, customizePath)] = originalHash;
+
+            // Write back to manifest
+            const yaml = require('yaml');
+            const updatedContent = yaml.stringify(manifestData, {
+              indent: 2,
+              lineWidth: 0,
+            });
+            await fs.writeFile(manifestPath, updatedContent, 'utf8');
           }
         }