diff --git a/x-pack/test/functional/apps/ml/index.ts b/x-pack/test/functional/apps/ml/index.ts
index 74dc0fc3ca9f0..29e852f96eea0 100644
--- a/x-pack/test/functional/apps/ml/index.ts
+++ b/x-pack/test/functional/apps/ml/index.ts
@@ -29,6 +29,7 @@ export default function ({ getService, loadTestFile }: FtrProviderContext) {
       await ml.testResources.deleteIndexPatternByTitle('ft_bank_marketing');
       await ml.testResources.deleteIndexPatternByTitle('ft_ihp_outlier');
       await ml.testResources.deleteIndexPatternByTitle('ft_egs_regression');
+      await ml.testResources.deleteIndexPatternByTitle('ft_module_sample_ecommerce');
       await esArchiver.unload('ml/farequote');
       await esArchiver.unload('ml/ecommerce');
       await esArchiver.unload('ml/categorization');
@@ -36,6 +37,7 @@ export default function ({ getService, loadTestFile }: FtrProviderContext) {
       await esArchiver.unload('ml/bm_classification');
       await esArchiver.unload('ml/ihp_outlier');
       await esArchiver.unload('ml/egs_regression');
+      await esArchiver.unload('ml/module_sample_ecommerce');
       await ml.testResources.resetKibanaTimeZone();
       await ml.securityUI.logout();
     });
diff --git a/x-pack/test/functional_basic/apps/ml/index.ts b/x-pack/test/functional_basic/apps/ml/index.ts
index 0e0c8cff17a4a..13a99b0818a52 100644
--- a/x-pack/test/functional_basic/apps/ml/index.ts
+++ b/x-pack/test/functional_basic/apps/ml/index.ts
@@ -27,9 +27,13 @@ export default function ({ getService, loadTestFile }: FtrProviderContext) {
       await ml.securityCommon.cleanMlUsers();
       await ml.securityCommon.cleanMlRoles();
 
+      await ml.testResources.deleteSavedSearches();
+
       await ml.testResources.deleteIndexPatternByTitle('ft_farequote');
+      await ml.testResources.deleteIndexPatternByTitle('ft_module_sample_ecommerce');
 
       await esArchiver.unload('ml/farequote');
+      await esArchiver.unload('ml/module_sample_ecommerce');
 
       await ml.testResources.resetKibanaTimeZone();
     });