diff --git a/packages/core/ui-settings/core-ui-settings-server-internal/src/clients/ui_settings_client.test.ts b/packages/core/ui-settings/core-ui-settings-server-internal/src/clients/ui_settings_client.test.ts
index 2612c8778898b..b00517d259a48 100644
--- a/packages/core/ui-settings/core-ui-settings-server-internal/src/clients/ui_settings_client.test.ts
+++ b/packages/core/ui-settings/core-ui-settings-server-internal/src/clients/ui_settings_client.test.ts
@@ -64,7 +64,12 @@ describe('ui settings', () => {
       await uiSettings.setMany({ one: 'value' });
 
       expect(savedObjectsClient.update).toHaveBeenCalledTimes(1);
-      expect(savedObjectsClient.update).toHaveBeenCalledWith(TYPE, ID, { one: 'value' });
+      expect(savedObjectsClient.update).toHaveBeenCalledWith(
+        TYPE,
+        ID,
+        { one: 'value' },
+        { refresh: false }
+      );
     });
 
     it('updates several values in one operation', async () => {
@@ -72,10 +77,15 @@ describe('ui settings', () => {
       await uiSettings.setMany({ one: 'value', another: 'val' });
 
       expect(savedObjectsClient.update).toHaveBeenCalledTimes(1);
-      expect(savedObjectsClient.update).toHaveBeenCalledWith(TYPE, ID, {
-        one: 'value',
-        another: 'val',
-      });
+      expect(savedObjectsClient.update).toHaveBeenCalledWith(
+        TYPE,
+        ID,
+        {
+          one: 'value',
+          another: 'val',
+        },
+        { refresh: false }
+      );
     });
 
     it('automatically creates the savedConfig if it is missing', async () => {
@@ -159,9 +169,14 @@ describe('ui settings', () => {
       await uiSettings.set('one', 'value');
 
       expect(savedObjectsClient.update).toHaveBeenCalledTimes(1);
-      expect(savedObjectsClient.update).toHaveBeenCalledWith(TYPE, ID, {
-        one: 'value',
-      });
+      expect(savedObjectsClient.update).toHaveBeenCalledWith(
+        TYPE,
+        ID,
+        {
+          one: 'value',
+        },
+        { refresh: false }
+      );
     });
 
     it('validates value if a schema presents', async () => {
@@ -202,7 +217,12 @@ describe('ui settings', () => {
       await uiSettings.remove('one');
 
       expect(savedObjectsClient.update).toHaveBeenCalledTimes(1);
-      expect(savedObjectsClient.update).toHaveBeenCalledWith(TYPE, ID, { one: null });
+      expect(savedObjectsClient.update).toHaveBeenCalledWith(
+        TYPE,
+        ID,
+        { one: null },
+        { refresh: false }
+      );
     });
 
     it('does not fail validation', async () => {
@@ -246,7 +266,12 @@ describe('ui settings', () => {
       await uiSettings.removeMany(['one']);
 
       expect(savedObjectsClient.update).toHaveBeenCalledTimes(1);
-      expect(savedObjectsClient.update).toHaveBeenCalledWith(TYPE, ID, { one: null });
+      expect(savedObjectsClient.update).toHaveBeenCalledWith(
+        TYPE,
+        ID,
+        { one: null },
+        { refresh: false }
+      );
     });
 
     it('updates several values in one operation', async () => {
@@ -254,11 +279,16 @@ describe('ui settings', () => {
       await uiSettings.removeMany(['one', 'two', 'three']);
 
       expect(savedObjectsClient.update).toHaveBeenCalledTimes(1);
-      expect(savedObjectsClient.update).toHaveBeenCalledWith(TYPE, ID, {
-        one: null,
-        two: null,
-        three: null,
-      });
+      expect(savedObjectsClient.update).toHaveBeenCalledWith(
+        TYPE,
+        ID,
+        {
+          one: null,
+          two: null,
+          three: null,
+        },
+        { refresh: false }
+      );
     });
 
     it('does not fail validation', async () => {
diff --git a/packages/core/ui-settings/core-ui-settings-server-internal/src/clients/ui_settings_client_common.ts b/packages/core/ui-settings/core-ui-settings-server-internal/src/clients/ui_settings_client_common.ts
index 992a851db99fd..d52644a0e8bfe 100644
--- a/packages/core/ui-settings/core-ui-settings-server-internal/src/clients/ui_settings_client_common.ts
+++ b/packages/core/ui-settings/core-ui-settings-server-internal/src/clients/ui_settings_client_common.ts
@@ -129,7 +129,7 @@ export abstract class UiSettingsClientCommon extends BaseUiSettingsClient {
     autoCreateOrUpgradeIfMissing?: boolean;
   }) {
     try {
-      await this.savedObjectsClient.update(this.type, this.id, changes);
+      await this.savedObjectsClient.update(this.type, this.id, changes, { refresh: false });
     } catch (error) {
       if (!SavedObjectsErrorHelpers.isNotFoundError(error) || !autoCreateOrUpgradeIfMissing) {
         throw error;
diff --git a/packages/core/ui-settings/core-ui-settings-server-internal/src/clients/ui_settings_global_client.test.ts b/packages/core/ui-settings/core-ui-settings-server-internal/src/clients/ui_settings_global_client.test.ts
index 2e4988f20c9df..56c3d53e2109f 100644
--- a/packages/core/ui-settings/core-ui-settings-server-internal/src/clients/ui_settings_global_client.test.ts
+++ b/packages/core/ui-settings/core-ui-settings-server-internal/src/clients/ui_settings_global_client.test.ts
@@ -86,9 +86,14 @@ describe('ui settings global client', () => {
       const { uiSettingsClient, savedObjectsClient } = setup();
       await uiSettingsClient.set('settingA', 'cde');
       expect(savedObjectsClient.update).toHaveBeenCalledTimes(1);
-      expect(savedObjectsClient.update).toHaveBeenCalledWith(TYPE, ID, {
-        settingA: 'cde',
-      });
+      expect(savedObjectsClient.update).toHaveBeenCalledWith(
+        TYPE,
+        ID,
+        {
+          settingA: 'cde',
+        },
+        { refresh: false }
+      );
     });
   });
 
diff --git a/packages/core/ui-settings/core-ui-settings-server-internal/src/create_or_upgrade_saved_config/create_or_upgrade_saved_config.test.ts b/packages/core/ui-settings/core-ui-settings-server-internal/src/create_or_upgrade_saved_config/create_or_upgrade_saved_config.test.ts
index 63a80e673a487..9f74929aaf2cc 100644
--- a/packages/core/ui-settings/core-ui-settings-server-internal/src/create_or_upgrade_saved_config/create_or_upgrade_saved_config.test.ts
+++ b/packages/core/ui-settings/core-ui-settings-server-internal/src/create_or_upgrade_saved_config/create_or_upgrade_saved_config.test.ts
@@ -79,6 +79,7 @@ describe('uiSettings/createOrUpgradeSavedConfig', function () {
         },
         {
           id: version,
+          refresh: false,
         }
       );
     });
@@ -110,6 +111,7 @@ describe('uiSettings/createOrUpgradeSavedConfig', function () {
         },
         {
           id: version,
+          refresh: false,
         }
       );
     });
@@ -140,7 +142,7 @@ describe('uiSettings/createOrUpgradeSavedConfig', function () {
           defaultIndex: 'another-index',
           isDefaultIndexMigrated: true,
         },
-        { id: version }
+        { id: version, refresh: false }
       );
     });
 
@@ -282,6 +284,7 @@ describe('uiSettings/createOrUpgradeSavedConfig', function () {
         },
         {
           id: version,
+          refresh: false,
         }
       );
     });
@@ -313,6 +316,7 @@ describe('uiSettings/createOrUpgradeSavedConfig', function () {
         },
         {
           id: version,
+          refresh: false,
         }
       );
     });
diff --git a/packages/core/ui-settings/core-ui-settings-server-internal/src/create_or_upgrade_saved_config/create_or_upgrade_saved_config.ts b/packages/core/ui-settings/core-ui-settings-server-internal/src/create_or_upgrade_saved_config/create_or_upgrade_saved_config.ts
index d6e0fffa05868..53ec0b78d3f89 100644
--- a/packages/core/ui-settings/core-ui-settings-server-internal/src/create_or_upgrade_saved_config/create_or_upgrade_saved_config.ts
+++ b/packages/core/ui-settings/core-ui-settings-server-internal/src/create_or_upgrade_saved_config/create_or_upgrade_saved_config.ts
@@ -63,7 +63,7 @@ export async function createOrUpgradeSavedConfig(
 
   try {
     // create the new SavedConfig
-    await savedObjectsClient.create(type, attributes, { id: version });
+    await savedObjectsClient.create(type, attributes, { id: version, refresh: false });
   } catch (error) {
     if (handleWriteErrors) {
       if (SavedObjectsErrorHelpers.isConflictError(error)) {
diff --git a/packages/kbn-es-archiver/src/actions/empty_kibana_index.ts b/packages/kbn-es-archiver/src/actions/empty_kibana_index.ts
index 2f02b51be5501..2c23eec3ca2aa 100644
--- a/packages/kbn-es-archiver/src/actions/empty_kibana_index.ts
+++ b/packages/kbn-es-archiver/src/actions/empty_kibana_index.ts
@@ -26,6 +26,7 @@ export async function emptyKibanaIndexAction({
 
   await cleanSavedObjectIndices({ client, stats, log });
   await migrateSavedObjectIndices(kbnClient);
+  await client.indices.refresh({ index: ALL_SAVED_OBJECT_INDICES });
   ALL_SAVED_OBJECT_INDICES.forEach((indexPattern) => stats.createdIndex(indexPattern));
   return stats.toJSON();
 }
diff --git a/src/core/server/integration_tests/ui_settings/doc_missing.ts b/src/core/server/integration_tests/ui_settings/doc_missing.ts
index b31514d4d11c8..4e04b0ecbd149 100644
--- a/src/core/server/integration_tests/ui_settings/doc_missing.ts
+++ b/src/core/server/integration_tests/ui_settings/doc_missing.ts
@@ -13,6 +13,8 @@ export const docMissingSuite = (savedObjectsIndex: string) => () => {
   beforeEach(async () => {
     const { esClient } = getServices();
 
+    await esClient.indices.refresh({ index: savedObjectsIndex });
+
     // delete all docs from kibana index to ensure savedConfig is not found
     await esClient.deleteByQuery({
       index: savedObjectsIndex,