diff --git a/x-pack/test/api_integration/apis/ml/modules/index.ts b/x-pack/test/api_integration/apis/ml/modules/index.ts
index 3cf1c7f7878402..c6a75eccfa4c83 100644
--- a/x-pack/test/api_integration/apis/ml/modules/index.ts
+++ b/x-pack/test/api_integration/apis/ml/modules/index.ts
@@ -8,6 +8,7 @@
 import { FtrProviderContext } from '../../../ftr_provider_context';
 
 export default function ({ getService, loadTestFile }: FtrProviderContext) {
+  const esArchiver = getService('esArchiver');
   const ml = getService('ml');
   const supertest = getService('supertest');
 
@@ -15,8 +16,12 @@ export default function ({ getService, loadTestFile }: FtrProviderContext) {
 
   describe('modules', function () {
     before(async () => {
+      // use empty_kibana to make sure the fleet setup is removed correctly after the tests
+      await esArchiver.load('x-pack/test/functional/es_archives/empty_kibana');
+
       // Fleet need to be setup to be able to setup packages
       await supertest.post(`/api/fleet/setup`).set({ 'kbn-xsrf': 'some-xsrf-token' }).expect(200);
+
       for (const fleetPackage of fleetPackages) {
         await ml.testResources.installFleetPackage(fleetPackage);
       }
@@ -26,6 +31,7 @@ export default function ({ getService, loadTestFile }: FtrProviderContext) {
       for (const fleetPackage of fleetPackages) {
         await ml.testResources.removeFleetPackage(fleetPackage);
       }
+      await esArchiver.unload('x-pack/test/functional/es_archives/empty_kibana');
     });
 
     loadTestFile(require.resolve('./get_module'));
diff --git a/x-pack/test/functional/services/ml/anomaly_explorer.ts b/x-pack/test/functional/services/ml/anomaly_explorer.ts
index 6ec45204388d7e..4392de7ee55677 100644
--- a/x-pack/test/functional/services/ml/anomaly_explorer.ts
+++ b/x-pack/test/functional/services/ml/anomaly_explorer.ts
@@ -10,6 +10,7 @@ import expect from '@kbn/expect';
 import { FtrProviderContext } from '../../ftr_provider_context';
 
 export function MachineLearningAnomalyExplorerProvider({ getService }: FtrProviderContext) {
+  const retry = getService('retry');
   const testSubjects = getService('testSubjects');
 
   return {
@@ -82,12 +83,8 @@ export function MachineLearningAnomalyExplorerProvider({ getService }: FtrProvid
     },
 
     async addAndEditSwimlaneInDashboard(dashboardTitle: string) {
-      await this.filterWithSearchString(dashboardTitle);
-      await testSubjects.isDisplayed('mlDashboardSelectionTable > checkboxSelectAll');
-      await testSubjects.clickWhenNotDisabled('mlDashboardSelectionTable > checkboxSelectAll');
-      expect(await testSubjects.isChecked('mlDashboardSelectionTable > checkboxSelectAll')).to.be(
-        true
-      );
+      await this.filterDashboardSearchWithSearchString(dashboardTitle);
+      await this.selectAllDashboards();
       await testSubjects.clickWhenNotDisabled('mlAddAndEditDashboardButton');
       // changing to the dashboard app might take sime time
       const embeddable = await testSubjects.find('mlAnomalySwimlaneEmbeddableWrapper', 30 * 1000);
@@ -106,11 +103,30 @@ export function MachineLearningAnomalyExplorerProvider({ getService }: FtrProvid
       await testSubjects.existOrFail('~mlDashboardSelectionTable', { timeout: 60 * 1000 });
     },
 
-    async filterWithSearchString(filter: string) {
+    async filterDashboardSearchWithSearchString(filter: string) {
       await this.waitForDashboardsToLoad();
       const searchBarInput = await testSubjects.find('mlDashboardsSearchBox');
       await searchBarInput.clearValueWithKeyboard();
       await searchBarInput.type(filter);
+      await this.assertDashboardSearchInputValue(filter);
+    },
+
+    async assertDashboardSearchInputValue(expectedSearchValue: string) {
+      const searchBarInput = await testSubjects.find('mlDashboardsSearchBox');
+      const actualSearchValue = await searchBarInput.getAttribute('value');
+      expect(actualSearchValue).to.eql(
+        expectedSearchValue,
+        `Dashboard search input value should be '${expectedSearchValue}' (got '${actualSearchValue}')`
+      );
+    },
+
+    async selectAllDashboards() {
+      await retry.tryForTime(3000, async () => {
+        await testSubjects.clickWhenNotDisabled('mlDashboardSelectionTable > checkboxSelectAll');
+        expect(
+          await testSubjects.isChecked('mlDashboardSelectionTable > checkboxSelectAll')
+        ).to.eql(true, 'Checkbox to select all dashboards should be selected');
+      });
     },
 
     async assertClearSelectionButtonVisible(expectVisible: boolean) {
diff --git a/x-pack/test/functional/services/ml/data_frame_analytics_creation.ts b/x-pack/test/functional/services/ml/data_frame_analytics_creation.ts
index b22748608589ed..ab3692be9288f0 100644
--- a/x-pack/test/functional/services/ml/data_frame_analytics_creation.ts
+++ b/x-pack/test/functional/services/ml/data_frame_analytics_creation.ts
@@ -404,42 +404,58 @@ export function MachineLearningDataFrameAnalyticsCreationProvider(
     },
 
     async assertConfigurationStepActive() {
-      await testSubjects.existOrFail('mlAnalyticsCreateJobWizardConfigurationStep active');
+      await testSubjects.existOrFail('mlAnalyticsCreateJobWizardConfigurationStep active', {
+        timeout: 3000,
+      });
     },
 
     async assertAdditionalOptionsStepActive() {
-      await testSubjects.existOrFail('mlAnalyticsCreateJobWizardAdvancedStep active');
+      await testSubjects.existOrFail('mlAnalyticsCreateJobWizardAdvancedStep active', {
+        timeout: 3000,
+      });
     },
 
     async assertDetailsStepActive() {
-      await testSubjects.existOrFail('mlAnalyticsCreateJobWizardDetailsStep active');
+      await testSubjects.existOrFail('mlAnalyticsCreateJobWizardDetailsStep active', {
+        timeout: 3000,
+      });
     },
 
     async assertCreateStepActive() {
-      await testSubjects.existOrFail('mlAnalyticsCreateJobWizardCreateStep active');
+      await testSubjects.existOrFail('mlAnalyticsCreateJobWizardCreateStep active', {
+        timeout: 3000,
+      });
     },
 
     async assertValidationStepActive() {
-      await testSubjects.existOrFail('mlAnalyticsCreateJobWizardValidationStepWrapper active');
+      await testSubjects.existOrFail('mlAnalyticsCreateJobWizardValidationStepWrapper active', {
+        timeout: 3000,
+      });
     },
 
     async continueToAdditionalOptionsStep() {
-      await retry.tryForTime(5000, async () => {
-        await testSubjects.clickWhenNotDisabled('mlAnalyticsCreateJobWizardContinueButton');
+      await retry.tryForTime(15 * 1000, async () => {
+        await testSubjects.clickWhenNotDisabled(
+          'mlAnalyticsCreateJobWizardConfigurationStep active > mlAnalyticsCreateJobWizardContinueButton'
+        );
         await this.assertAdditionalOptionsStepActive();
       });
     },
 
     async continueToDetailsStep() {
-      await retry.tryForTime(5000, async () => {
-        await testSubjects.clickWhenNotDisabled('mlAnalyticsCreateJobWizardContinueButton');
+      await retry.tryForTime(15 * 1000, async () => {
+        await testSubjects.clickWhenNotDisabled(
+          'mlAnalyticsCreateJobWizardAdvancedStep active > mlAnalyticsCreateJobWizardContinueButton'
+        );
         await this.assertDetailsStepActive();
       });
     },
 
     async continueToValidationStep() {
-      await retry.tryForTime(5000, async () => {
-        await testSubjects.clickWhenNotDisabled('mlAnalyticsCreateJobWizardContinueButton');
+      await retry.tryForTime(15 * 1000, async () => {
+        await testSubjects.clickWhenNotDisabled(
+          'mlAnalyticsCreateJobWizardDetailsStep active > mlAnalyticsCreateJobWizardContinueButton'
+        );
         await this.assertValidationStepActive();
       });
     },
@@ -456,8 +472,10 @@ export function MachineLearningDataFrameAnalyticsCreationProvider(
     },
 
     async continueToCreateStep() {
-      await retry.tryForTime(5000, async () => {
-        await testSubjects.clickWhenNotDisabled('mlAnalyticsCreateJobWizardContinueButton');
+      await retry.tryForTime(15 * 1000, async () => {
+        await testSubjects.clickWhenNotDisabled(
+          'mlAnalyticsCreateJobWizardValidationStepWrapper active > mlAnalyticsCreateJobWizardContinueButton'
+        );
         await this.assertCreateStepActive();
       });
     },