diff --git a/x-pack/plugins/ingest_manager/server/services/epm/elasticsearch/ingest_pipeline/install.ts b/x-pack/plugins/ingest_manager/server/services/epm/elasticsearch/ingest_pipeline/install.ts
index 43c0179c0aa8a..58abdeb0d443d 100644
--- a/x-pack/plugins/ingest_manager/server/services/epm/elasticsearch/ingest_pipeline/install.ts
+++ b/x-pack/plugins/ingest_manager/server/services/epm/elasticsearch/ingest_pipeline/install.ts
@@ -14,6 +14,8 @@ import {
 import * as Registry from '../../registry';
 import { CallESAsCurrentUser } from '../../../../types';
 import { saveInstalledEsRefs } from '../../packages/install';
+import { getInstallationObject } from '../../packages';
+import { deletePipelineRefs } from './remove';
 
 interface RewriteSubstitution {
   source: string;
@@ -31,6 +33,7 @@ export const installPipelines = async (
   // it can be created pointing to the new template, without removing the old one and effecting data
   // so do not remove the currently installed pipelines here
   const dataStreams = installablePackage.data_streams;
+  const { name: pkgName, version: pkgVersion } = installablePackage;
   if (!dataStreams?.length) return [];
   const pipelinePaths = paths.filter((path) => isPipeline(path));
   // get and save pipeline refs before installing pipelines
@@ -50,6 +53,20 @@ export const installPipelines = async (
     acc.push(...pipelineObjectRefs);
     return acc;
   }, []);
+
+  // check that we don't duplicate the pipeline refs if the user is reinstalling
+  const installedPkg = await getInstallationObject({
+    savedObjectsClient,
+    pkgName,
+  });
+  if (!installedPkg) throw new Error("integration wasn't found while installing pipelines");
+  // remove the current pipeline refs, if any exist, associated with this version before saving new ones so no duplicates occur
+  await deletePipelineRefs(
+    savedObjectsClient,
+    installedPkg.attributes.installed_es,
+    pkgName,
+    pkgVersion
+  );
   await saveInstalledEsRefs(savedObjectsClient, installablePackage.name, pipelineRefs);
   const pipelines = dataStreams.reduce<Array<Promise<EsAssetReference[]>>>((acc, dataStream) => {
     if (dataStream.ingest_pipeline) {
diff --git a/x-pack/test/ingest_manager_api_integration/apis/epm/install_remove_assets.ts b/x-pack/test/ingest_manager_api_integration/apis/epm/install_remove_assets.ts
index cc6a384dcaafe..72ea9cb4e7ef3 100644
--- a/x-pack/test/ingest_manager_api_integration/apis/epm/install_remove_assets.ts
+++ b/x-pack/test/ingest_manager_api_integration/apis/epm/install_remove_assets.ts
@@ -5,6 +5,8 @@
  */
 
 import expect from '@kbn/expect';
+import { sortBy } from 'lodash';
+import { AssetReference } from '../../../../plugins/ingest_manager/common';
 import { FtrProviderContext } from '../../../api_integration/ftr_provider_context';
 import { skipIfNoDockerRegistry } from '../../helpers';
 
@@ -12,6 +14,8 @@ export default function (providerContext: FtrProviderContext) {
   const { getService } = providerContext;
   const kibanaServer = getService('kibanaServer');
   const supertest = getService('supertest');
+  const dockerServers = getService('dockerServers');
+  const server = dockerServers.get('registry');
   const es = getService('es');
   const pkgName = 'all_assets';
   const pkgVersion = '0.1.0';
@@ -33,194 +37,27 @@ export default function (providerContext: FtrProviderContext) {
     describe('installs all assets when installing a package for the first time', async () => {
       skipIfNoDockerRegistry(providerContext);
       before(async () => {
+        if (!server.enabled) return;
         await installPackage(pkgKey);
       });
       after(async () => {
+        if (!server.enabled) return;
         await uninstallPackage(pkgKey);
       });
-      it('should have installed the ILM policy', async function () {
-        const resPolicy = await es.transport.request({
-          method: 'GET',
-          path: `/_ilm/policy/all_assets`,
-        });
-        expect(resPolicy.statusCode).equal(200);
-      });
-      it('should have installed the index templates', async function () {
-        const resLogsTemplate = await es.transport.request({
-          method: 'GET',
-          path: `/_index_template/${logsTemplateName}`,
-        });
-        expect(resLogsTemplate.statusCode).equal(200);
-
-        const resMetricsTemplate = await es.transport.request({
-          method: 'GET',
-          path: `/_index_template/${metricsTemplateName}`,
-        });
-        expect(resMetricsTemplate.statusCode).equal(200);
-      });
-      it('should have installed the pipelines', async function () {
-        const res = await es.transport.request({
-          method: 'GET',
-          path: `/_ingest/pipeline/${logsTemplateName}-${pkgVersion}`,
-        });
-        expect(res.statusCode).equal(200);
-        const resPipeline1 = await es.transport.request({
-          method: 'GET',
-          path: `/_ingest/pipeline/${logsTemplateName}-${pkgVersion}-pipeline1`,
-        });
-        expect(resPipeline1.statusCode).equal(200);
-        const resPipeline2 = await es.transport.request({
-          method: 'GET',
-          path: `/_ingest/pipeline/${logsTemplateName}-${pkgVersion}-pipeline2`,
-        });
-        expect(resPipeline2.statusCode).equal(200);
-      });
-      it('should have installed the template components', async function () {
-        const res = await es.transport.request({
-          method: 'GET',
-          path: `/_component_template/${logsTemplateName}-mappings`,
-        });
-        expect(res.statusCode).equal(200);
-        const resSettings = await es.transport.request({
-          method: 'GET',
-          path: `/_component_template/${logsTemplateName}-settings`,
-        });
-        expect(resSettings.statusCode).equal(200);
-      });
-      it('should have installed the transform components', async function () {
-        const res = await es.transport.request({
-          method: 'GET',
-          path: `/_transform/${pkgName}.test-default-${pkgVersion}`,
-        });
-        expect(res.statusCode).equal(200);
-      });
-      it('should have created the index for the transform', async function () {
-        // the  index is defined in the transform file
-        const res = await es.transport.request({
-          method: 'GET',
-          path: `/logs-all_assets.test_log_current_default`,
-        });
-        expect(res.statusCode).equal(200);
-      });
-      it('should have installed the kibana assets', async function () {
-        const resIndexPatternLogs = await kibanaServer.savedObjects.get({
-          type: 'index-pattern',
-          id: 'logs-*',
-        });
-        expect(resIndexPatternLogs.id).equal('logs-*');
-        const resIndexPatternMetrics = await kibanaServer.savedObjects.get({
-          type: 'index-pattern',
-          id: 'metrics-*',
-        });
-        expect(resIndexPatternMetrics.id).equal('metrics-*');
-        const resDashboard = await kibanaServer.savedObjects.get({
-          type: 'dashboard',
-          id: 'sample_dashboard',
-        });
-        expect(resDashboard.id).equal('sample_dashboard');
-        const resDashboard2 = await kibanaServer.savedObjects.get({
-          type: 'dashboard',
-          id: 'sample_dashboard2',
-        });
-        expect(resDashboard2.id).equal('sample_dashboard2');
-        const resVis = await kibanaServer.savedObjects.get({
-          type: 'visualization',
-          id: 'sample_visualization',
-        });
-        expect(resVis.id).equal('sample_visualization');
-        const resSearch = await kibanaServer.savedObjects.get({
-          type: 'search',
-          id: 'sample_search',
-        });
-        expect(resSearch.id).equal('sample_search');
-      });
-      it('should create an index pattern with the package fields', async () => {
-        const resIndexPatternLogs = await kibanaServer.savedObjects.get({
-          type: 'index-pattern',
-          id: 'logs-*',
-        });
-        const fields = JSON.parse(resIndexPatternLogs.attributes.fields);
-        const exists = fields.find((field: { name: string }) => field.name === 'logs_test_name');
-        expect(exists).not.to.be(undefined);
-        const resIndexPatternMetrics = await kibanaServer.savedObjects.get({
-          type: 'index-pattern',
-          id: 'metrics-*',
-        });
-        const fieldsMetrics = JSON.parse(resIndexPatternMetrics.attributes.fields);
-        const metricsExists = fieldsMetrics.find(
-          (field: { name: string }) => field.name === 'metrics_test_name'
-        );
-        expect(metricsExists).not.to.be(undefined);
-      });
-      it('should have created the correct saved object', async function () {
-        const res = await kibanaServer.savedObjects.get({
-          type: 'epm-packages',
-          id: 'all_assets',
-        });
-        expect(res.attributes).eql({
-          installed_kibana: [
-            {
-              id: 'sample_dashboard',
-              type: 'dashboard',
-            },
-            {
-              id: 'sample_dashboard2',
-              type: 'dashboard',
-            },
-            {
-              id: 'sample_search',
-              type: 'search',
-            },
-            {
-              id: 'sample_visualization',
-              type: 'visualization',
-            },
-          ],
-          installed_es: [
-            {
-              id: 'logs-all_assets.test_logs-0.1.0',
-              type: 'ingest_pipeline',
-            },
-            {
-              id: 'logs-all_assets.test_logs-0.1.0-pipeline1',
-              type: 'ingest_pipeline',
-            },
-            {
-              id: 'logs-all_assets.test_logs-0.1.0-pipeline2',
-              type: 'ingest_pipeline',
-            },
-            {
-              id: 'logs-all_assets.test_logs',
-              type: 'index_template',
-            },
-            {
-              id: 'metrics-all_assets.test_metrics',
-              type: 'index_template',
-            },
-            {
-              id: 'all_assets.test-default-0.1.0',
-              type: 'transform',
-            },
-          ],
-          es_index_patterns: {
-            test_logs: 'logs-all_assets.test_logs-*',
-            test_metrics: 'metrics-all_assets.test_metrics-*',
-          },
-          name: 'all_assets',
-          version: '0.1.0',
-          internal: false,
-          removable: true,
-          install_version: '0.1.0',
-          install_status: 'installed',
-          install_started_at: res.attributes.install_started_at,
-          install_source: 'registry',
-        });
+      expectAssetsInstalled({
+        logsTemplateName,
+        metricsTemplateName,
+        pkgVersion,
+        pkgName,
+        es,
+        kibanaServer,
       });
     });
 
     describe('uninstalls all assets when uninstalling a package', async () => {
       skipIfNoDockerRegistry(providerContext);
       before(async () => {
+        if (!server.enabled) return;
         // these tests ensure that uninstall works properly so make sure that the package gets installed and uninstalled
         // and then we'll test that not artifacts are left behind.
         await installPackage(pkgKey);
@@ -403,5 +240,228 @@ export default function (providerContext: FtrProviderContext) {
         expect(res.response.data.statusCode).equal(404);
       });
     });
+
+    describe('reinstalls all assets', async () => {
+      skipIfNoDockerRegistry(providerContext);
+      before(async () => {
+        if (!server.enabled) return;
+        await installPackage(pkgKey);
+        // reinstall
+        await installPackage(pkgKey);
+      });
+      after(async () => {
+        if (!server.enabled) return;
+        await uninstallPackage(pkgKey);
+      });
+      expectAssetsInstalled({
+        logsTemplateName,
+        metricsTemplateName,
+        pkgVersion,
+        pkgName,
+        es,
+        kibanaServer,
+      });
+    });
   });
 }
+
+const expectAssetsInstalled = ({
+  logsTemplateName,
+  metricsTemplateName,
+  pkgVersion,
+  pkgName,
+  es,
+  kibanaServer,
+}: {
+  logsTemplateName: string;
+  metricsTemplateName: string;
+  pkgVersion: string;
+  pkgName: string;
+  es: any;
+  kibanaServer: any;
+}) => {
+  it('should have installed the ILM policy', async function () {
+    const resPolicy = await es.transport.request({
+      method: 'GET',
+      path: `/_ilm/policy/all_assets`,
+    });
+    expect(resPolicy.statusCode).equal(200);
+  });
+  it('should have installed the index templates', async function () {
+    const resLogsTemplate = await es.transport.request({
+      method: 'GET',
+      path: `/_index_template/${logsTemplateName}`,
+    });
+    expect(resLogsTemplate.statusCode).equal(200);
+
+    const resMetricsTemplate = await es.transport.request({
+      method: 'GET',
+      path: `/_index_template/${metricsTemplateName}`,
+    });
+    expect(resMetricsTemplate.statusCode).equal(200);
+  });
+  it('should have installed the pipelines', async function () {
+    const res = await es.transport.request({
+      method: 'GET',
+      path: `/_ingest/pipeline/${logsTemplateName}-${pkgVersion}`,
+    });
+    expect(res.statusCode).equal(200);
+    const resPipeline1 = await es.transport.request({
+      method: 'GET',
+      path: `/_ingest/pipeline/${logsTemplateName}-${pkgVersion}-pipeline1`,
+    });
+    expect(resPipeline1.statusCode).equal(200);
+    const resPipeline2 = await es.transport.request({
+      method: 'GET',
+      path: `/_ingest/pipeline/${logsTemplateName}-${pkgVersion}-pipeline2`,
+    });
+    expect(resPipeline2.statusCode).equal(200);
+  });
+  it('should have installed the template components', async function () {
+    const res = await es.transport.request({
+      method: 'GET',
+      path: `/_component_template/${logsTemplateName}-mappings`,
+    });
+    expect(res.statusCode).equal(200);
+    const resSettings = await es.transport.request({
+      method: 'GET',
+      path: `/_component_template/${logsTemplateName}-settings`,
+    });
+    expect(resSettings.statusCode).equal(200);
+  });
+  it('should have installed the transform components', async function () {
+    const res = await es.transport.request({
+      method: 'GET',
+      path: `/_transform/${pkgName}.test-default-${pkgVersion}`,
+    });
+    expect(res.statusCode).equal(200);
+  });
+  it('should have created the index for the transform', async function () {
+    // the  index is defined in the transform file
+    const res = await es.transport.request({
+      method: 'GET',
+      path: `/logs-all_assets.test_log_current_default`,
+    });
+    expect(res.statusCode).equal(200);
+  });
+  it('should have installed the kibana assets', async function () {
+    const resIndexPatternLogs = await kibanaServer.savedObjects.get({
+      type: 'index-pattern',
+      id: 'logs-*',
+    });
+    expect(resIndexPatternLogs.id).equal('logs-*');
+    const resIndexPatternMetrics = await kibanaServer.savedObjects.get({
+      type: 'index-pattern',
+      id: 'metrics-*',
+    });
+    expect(resIndexPatternMetrics.id).equal('metrics-*');
+    const resDashboard = await kibanaServer.savedObjects.get({
+      type: 'dashboard',
+      id: 'sample_dashboard',
+    });
+    expect(resDashboard.id).equal('sample_dashboard');
+    const resDashboard2 = await kibanaServer.savedObjects.get({
+      type: 'dashboard',
+      id: 'sample_dashboard2',
+    });
+    expect(resDashboard2.id).equal('sample_dashboard2');
+    const resVis = await kibanaServer.savedObjects.get({
+      type: 'visualization',
+      id: 'sample_visualization',
+    });
+    expect(resVis.id).equal('sample_visualization');
+    const resSearch = await kibanaServer.savedObjects.get({
+      type: 'search',
+      id: 'sample_search',
+    });
+    expect(resSearch.id).equal('sample_search');
+  });
+  it('should create an index pattern with the package fields', async () => {
+    const resIndexPatternLogs = await kibanaServer.savedObjects.get({
+      type: 'index-pattern',
+      id: 'logs-*',
+    });
+    const fields = JSON.parse(resIndexPatternLogs.attributes.fields);
+    const exists = fields.find((field: { name: string }) => field.name === 'logs_test_name');
+    expect(exists).not.to.be(undefined);
+    const resIndexPatternMetrics = await kibanaServer.savedObjects.get({
+      type: 'index-pattern',
+      id: 'metrics-*',
+    });
+    const fieldsMetrics = JSON.parse(resIndexPatternMetrics.attributes.fields);
+    const metricsExists = fieldsMetrics.find(
+      (field: { name: string }) => field.name === 'metrics_test_name'
+    );
+    expect(metricsExists).not.to.be(undefined);
+  });
+  it('should have created the correct saved object', async function () {
+    const res = await kibanaServer.savedObjects.get({
+      type: 'epm-packages',
+      id: 'all_assets',
+    });
+    // during a reinstall the items can change
+    const sortedRes = {
+      ...res.attributes,
+      installed_kibana: sortBy(res.attributes.installed_kibana, (o: AssetReference) => o.type),
+      installed_es: sortBy(res.attributes.installed_es, (o: AssetReference) => o.type),
+    };
+    expect(sortedRes).eql({
+      installed_kibana: [
+        {
+          id: 'sample_dashboard',
+          type: 'dashboard',
+        },
+        {
+          id: 'sample_dashboard2',
+          type: 'dashboard',
+        },
+        {
+          id: 'sample_search',
+          type: 'search',
+        },
+        {
+          id: 'sample_visualization',
+          type: 'visualization',
+        },
+      ],
+      installed_es: [
+        {
+          id: 'logs-all_assets.test_logs',
+          type: 'index_template',
+        },
+        {
+          id: 'metrics-all_assets.test_metrics',
+          type: 'index_template',
+        },
+        {
+          id: 'logs-all_assets.test_logs-0.1.0',
+          type: 'ingest_pipeline',
+        },
+        {
+          id: 'logs-all_assets.test_logs-0.1.0-pipeline1',
+          type: 'ingest_pipeline',
+        },
+        {
+          id: 'logs-all_assets.test_logs-0.1.0-pipeline2',
+          type: 'ingest_pipeline',
+        },
+        {
+          id: 'all_assets.test-default-0.1.0',
+          type: 'transform',
+        },
+      ],
+      es_index_patterns: {
+        test_logs: 'logs-all_assets.test_logs-*',
+        test_metrics: 'metrics-all_assets.test_metrics-*',
+      },
+      name: 'all_assets',
+      version: '0.1.0',
+      internal: false,
+      removable: true,
+      install_version: '0.1.0',
+      install_status: 'installed',
+      install_started_at: res.attributes.install_started_at,
+      install_source: 'registry',
+    });
+  });
+};