diff --git a/pkg/workflow/safe_outputs_config_generation.go b/pkg/workflow/safe_outputs_config_generation.go
index b25fd9b0ae5..b5e13bf2027 100644
--- a/pkg/workflow/safe_outputs_config_generation.go
+++ b/pkg/workflow/safe_outputs_config_generation.go
@@ -33,13 +33,21 @@ func generateSafeOutputsConfig(data *WorkflowData) (string, error) {
 	safeOutputsConfigLog.Print("Generating safe outputs configuration for workflow")
 
 	safeOutputsConfig := make(map[string]any)
+	engineManifestFiles, engineManifestPathPrefixes := getEngineAgentFileInfoFromWorkflowData(data)
 
 	// Standard handler configs — sourced from handlerRegistry (same as GH_AW_SAFE_OUTPUTS_HANDLER_CONFIG)
 	for handlerName, builder := range handlerRegistry {
 		if handlerCfg := builder(data.SafeOutputs); handlerCfg != nil {
+			excludeFiles := extractStringSliceFromConfig(handlerCfg, "_protected_files_exclude")
 			// Strip the internal sentinel key used by the handler manager for compile-time
 			// exclusion processing — it must not be forwarded to the runtime config.json.
 			delete(handlerCfg, "_protected_files_exclude")
+			if _, hasProtectedFiles := handlerCfg["protected_files"]; hasProtectedFiles {
+				fullManifestFiles := getAllManifestFiles(engineManifestFiles...)
+				fullPathPrefixes := getProtectedPathPrefixes(engineManifestPathPrefixes...)
+				handlerCfg["protected_files"] = excludeFromSlice(fullManifestFiles, excludeFiles...)
+				handlerCfg["protected_path_prefixes"] = excludeFromSlice(fullPathPrefixes, excludeFiles...)
+			}
 			safeOutputsConfig[handlerName] = handlerCfg
 		}
 	}
@@ -195,6 +203,29 @@ func generateSafeOutputsConfig(data *WorkflowData) (string, error) {
 	return string(configJSON), nil
 }
 
+func getEngineAgentFileInfoFromWorkflowData(data *WorkflowData) (manifestFiles []string, pathPrefixes []string) {
+	if data == nil || data.EngineConfig == nil {
+		return nil, nil
+	}
+
+	engineRegistry := GetGlobalEngineRegistry()
+	engine, err := engineRegistry.GetEngine(data.EngineConfig.ID)
+	if err != nil {
+		safeOutputsConfigLog.Printf("Engine lookup failed for %q: %v — skipping agent manifest file injection", data.EngineConfig.ID, err)
+		return nil, nil
+	}
+	if engine == nil {
+		return nil, nil
+	}
+
+	provider, ok := engine.(AgentFileProvider)
+	if !ok {
+		return nil, nil
+	}
+
+	return provider.GetAgentManifestFiles(), provider.GetAgentManifestPathPrefixes()
+}
+
 // generateCustomJobToolDefinition creates an MCP tool definition for a custom safe-output job.
 // Returns a map representing the tool definition in MCP format with name, description, and inputSchema.
 func generateCustomJobToolDefinition(jobName string, jobConfig *SafeJobConfig) map[string]any {
diff --git a/pkg/workflow/safe_outputs_config_generation_test.go b/pkg/workflow/safe_outputs_config_generation_test.go
index 61e4aa36a66..c6f36a6697f 100644
--- a/pkg/workflow/safe_outputs_config_generation_test.go
+++ b/pkg/workflow/safe_outputs_config_generation_test.go
@@ -520,6 +520,64 @@ func TestGenerateSafeOutputsConfigCreatePullRequestBackwardCompat(t *testing.T)
 	assert.False(t, hasAllowedRepos, "allowed_repos should not be present when not configured")
 }
 
+func TestGenerateSafeOutputsConfigCreatePullRequestIncludesEngineManifests(t *testing.T) {
+	data := &WorkflowData{
+		EngineConfig: &EngineConfig{ID: "claude"},
+		SafeOutputs: &SafeOutputsConfig{
+			CreatePullRequests: &CreatePullRequestsConfig{
+				BaseSafeOutputConfig: BaseSafeOutputConfig{Max: strPtr("1")},
+			},
+		},
+	}
+
+	result, err := generateSafeOutputsConfig(data)
+	require.NoError(t, err, "generateSafeOutputsConfig should not return an error")
+	require.NotEmpty(t, result, "Expected non-empty config")
+
+	var parsed map[string]any
+	require.NoError(t, json.Unmarshal([]byte(result), &parsed), "Result must be valid JSON")
+
+	prConfig, ok := parsed["create_pull_request"].(map[string]any)
+	require.True(t, ok, "Expected create_pull_request key in config")
+
+	protectedFiles := parseStringSliceAny(prConfig["protected_files"], nil)
+	assert.Contains(t, protectedFiles, "CLAUDE.md", "CLAUDE.md should be protected for Claude engine workflows")
+	assert.Contains(t, protectedFiles, "AGENTS.md", "AGENTS.md should be protected for Claude engine workflows")
+
+	protectedPathPrefixes := parseStringSliceAny(prConfig["protected_path_prefixes"], nil)
+	assert.Contains(t, protectedPathPrefixes, ".claude/", ".claude/ should be protected for Claude engine workflows")
+}
+
+func TestGenerateSafeOutputsConfigCreatePullRequestAppliesProtectedFilesExclude(t *testing.T) {
+	data := &WorkflowData{
+		EngineConfig: &EngineConfig{ID: "claude"},
+		SafeOutputs: &SafeOutputsConfig{
+			CreatePullRequests: &CreatePullRequestsConfig{
+				BaseSafeOutputConfig:  BaseSafeOutputConfig{Max: strPtr("1")},
+				ProtectedFilesExclude: []string{"CLAUDE.md", ".claude/"},
+			},
+		},
+	}
+
+	result, err := generateSafeOutputsConfig(data)
+	require.NoError(t, err, "generateSafeOutputsConfig should not return an error")
+	require.NotEmpty(t, result, "Expected non-empty config")
+
+	var parsed map[string]any
+	require.NoError(t, json.Unmarshal([]byte(result), &parsed), "Result must be valid JSON")
+
+	prConfig, ok := parsed["create_pull_request"].(map[string]any)
+	require.True(t, ok, "Expected create_pull_request key in config")
+
+	protectedFiles := parseStringSliceAny(prConfig["protected_files"], nil)
+	assert.NotContains(t, protectedFiles, "CLAUDE.md", "CLAUDE.md should be excluded from protected_files")
+	assert.Contains(t, protectedFiles, "AGENTS.md", "AGENTS.md should remain in protected_files")
+
+	protectedPathPrefixes := parseStringSliceAny(prConfig["protected_path_prefixes"], nil)
+	assert.NotContains(t, protectedPathPrefixes, ".claude/", ".claude/ should be excluded from protected_path_prefixes")
+	assert.Contains(t, protectedPathPrefixes, ".github/", ".github/ should remain protected")
+}
+
 // TestGenerateSafeOutputsConfigCreatePullRequestAutoCloseIssue tests that auto_close_issue
 // is correctly serialized into config.json for create_pull_request.
 func TestGenerateSafeOutputsConfigCreatePullRequestAutoCloseIssue(t *testing.T) {