diff --git a/app_dart/integration_test/common.dart b/app_dart/integration_test/common.dart
index a2668516a..92e3f45e7 100644
--- a/app_dart/integration_test/common.dart
+++ b/app_dart/integration_test/common.dart
@@ -18,7 +18,7 @@ void expectNoDiff(String path) {
 
 /// Wrapper class to make it easy to add new repos + branches to the validation suite.
 class SupportedConfig {
-  SupportedConfig(this.slug, [this.branch = 'master']);
+  SupportedConfig(this.slug, [this.branch = 'main']);
 
   final RepositorySlug slug;
   final String branch;
diff --git a/app_dart/integration_test/validate_all_ci_configs_test.dart b/app_dart/integration_test/validate_all_ci_configs_test.dart
index 2032f5606..a5f79d683 100644
--- a/app_dart/integration_test/validate_all_ci_configs_test.dart
+++ b/app_dart/integration_test/validate_all_ci_configs_test.dart
@@ -18,10 +18,10 @@ import 'common.dart';
 
 /// List of repositories that have supported .ci.yaml config files.
 final List<SupportedConfig> configs = <SupportedConfig>[
-  SupportedConfig(RepositorySlug('flutter', 'cocoon'), 'main'),
-  SupportedConfig(RepositorySlug('flutter', 'engine'), 'main'),
+  SupportedConfig(RepositorySlug('flutter', 'cocoon')),
+  SupportedConfig(RepositorySlug('flutter', 'engine')),
   SupportedConfig(RepositorySlug('flutter', 'flutter')),
-  SupportedConfig(RepositorySlug('flutter', 'packages'), 'main'),
+  SupportedConfig(RepositorySlug('flutter', 'packages')),
 ];
 
 Future<void> main() async {
@@ -57,6 +57,13 @@ Future<void> main() async {
         );
         final YamlMap configYaml = loadYaml(configContent) as YamlMap;
         final pb.SchedulerConfig schedulerConfig = pb.SchedulerConfig()..mergeFromProto3Json(configYaml);
+        // Validate using the existing CiYaml logic.
+        CiYaml(
+          slug: config.slug,
+          branch: config.branch,
+          config: schedulerConfig,
+          validate: true,
+        );
 
         final List<String> githubBranches = getBranchesForRepository(config.slug);
 
@@ -81,11 +88,6 @@ Future<void> main() async {
           }
         }
 
-        if (config.slug.name == 'engine') {
-          print(githubBranches);
-          print(validEnabledBranches);
-        }
-
         // Verify the enabled branches
         for (String enabledBranch in validEnabledBranches.keys) {
           expect(
@@ -95,7 +97,6 @@ Future<void> main() async {
           );
         }
       },
-      skip: config.slug.name == 'flutter',
     );
   }
 }
diff --git a/app_dart/lib/src/model/ci_yaml/ci_yaml.dart b/app_dart/lib/src/model/ci_yaml/ci_yaml.dart
index 46f18321b..38cc3fda1 100644
--- a/app_dart/lib/src/model/ci_yaml/ci_yaml.dart
+++ b/app_dart/lib/src/model/ci_yaml/ci_yaml.dart
@@ -204,6 +204,7 @@ class CiYaml {
   ///   5. [pb.Target] should not depend on self
   ///   6. [pb.Target] cannot have more than 1 dependency
   ///   7. [pb.Target] should depend on target that already exist in depedency graph, and already recorded in map [targetGraph]
+  ///   8. [pb.Target] has an empty runIf or the runIf includes `.ci.yaml` and `DEPS if on the engine repo.
   void _validate(pb.SchedulerConfig schedulerConfig, String branch, {pb.SchedulerConfig? totSchedulerConfig}) {
     if (schedulerConfig.targets.isEmpty) {
       throw const FormatException('Scheduler config must have at least 1 target');
@@ -251,6 +252,15 @@ class CiYaml {
             }
           }
         }
+        // Verify runIf includes foundational files.
+        if (target.runIf.isNotEmpty) {
+          if (!target.runIf.contains('.ci.yaml')) {
+            exceptions.add('ERROR: ${target.name} is missing `.ci.yaml` in runIf');
+          }
+          if (slug == Config.engineSlug && !target.runIf.contains('DEPS')) {
+            exceptions.add('ERROR: ${target.name} is missing `DEPS` in runIf');
+          }
+        }
       }
 
       /// Check the dependencies for the current target if it is viable and to
diff --git a/app_dart/test/service/scheduler_test.dart b/app_dart/test/service/scheduler_test.dart
index fdc460416..53dd4b0be 100644
--- a/app_dart/test/service/scheduler_test.dart
+++ b/app_dart/test/service/scheduler_test.dart
@@ -55,6 +55,7 @@ targets:
     scheduler: luci
   - name: Linux runIf
     runIf:
+      - .ci.yaml
       - dev/**
   - name: Google Internal Roll
     postsubmit: true
@@ -708,6 +709,8 @@ targets:
       presubmit: true
       scheduler: luci
       runIf:
+        - .ci.yaml
+        - DEPS
         - dev/run_if/**
     - name: Linux Conditional Presubmit (runIfNot)
       presubmit: true