diff --git a/src/plugins/data/public/query/filter_manager/filter_manager.test.ts b/src/plugins/data/public/query/filter_manager/filter_manager.test.ts
index 1ade48b3537c8..8c790ac2ddc46 100644
--- a/src/plugins/data/public/query/filter_manager/filter_manager.test.ts
+++ b/src/plugins/data/public/query/filter_manager/filter_manager.test.ts
@@ -29,9 +29,16 @@ import { esFilters } from '../../../common';
 import { coreMock } from '../../../../../core/public/mocks';
 const setupMock = coreMock.createSetup();
 
-setupMock.uiSettings.get.mockImplementation((key: string) => {
-  return true;
-});
+const uiSettingsMock = (pinnedByDefault: boolean) => (key: string) => {
+  switch (key) {
+    case 'filters:pinnedByDefault':
+      return pinnedByDefault;
+    default:
+      throw new Error(`Unexpected uiSettings key in FilterManager mock: ${key}`);
+  }
+};
+
+setupMock.uiSettings.get.mockImplementation(uiSettingsMock(true));
 
 describe('filter_manager', () => {
   let updateSubscription: Subscription | undefined;
@@ -224,6 +231,44 @@ describe('filter_manager', () => {
       expect(newGlobalFilters).toHaveLength(2);
       expect(newAppFilters).toHaveLength(1);
     });
+
+    test('set filter with no state, and force pin', async () => {
+      const f1 = getFilter(esFilters.FilterStateStore.GLOBAL_STATE, false, false, 'age', 38);
+      f1.$state = undefined;
+
+      filterManager.setFilters([f1], true);
+      expect(filterManager.getGlobalFilters()).toHaveLength(1);
+      expect(filterManager.getAppFilters()).toHaveLength(0);
+    });
+
+    test('set filter with no state, and no pin', async () => {
+      const f1 = getFilter(esFilters.FilterStateStore.GLOBAL_STATE, false, false, 'age', 38);
+      f1.$state = undefined;
+
+      filterManager.setFilters([f1], false);
+      expect(filterManager.getGlobalFilters()).toHaveLength(0);
+      expect(filterManager.getAppFilters()).toHaveLength(1);
+    });
+
+    test('set filters with default pin', async () => {
+      const f1 = getFilter(esFilters.FilterStateStore.GLOBAL_STATE, false, false, 'age', 38);
+      f1.$state = undefined;
+      setupMock.uiSettings.get.mockImplementationOnce(uiSettingsMock(true));
+
+      filterManager.setFilters([f1]);
+      expect(filterManager.getGlobalFilters()).toHaveLength(1);
+      expect(filterManager.getAppFilters()).toHaveLength(0);
+    });
+
+    test('set filters without default pin', async () => {
+      const f1 = getFilter(esFilters.FilterStateStore.GLOBAL_STATE, false, false, 'age', 38);
+      f1.$state = undefined;
+
+      setupMock.uiSettings.get.mockImplementationOnce(uiSettingsMock(false));
+      filterManager.setFilters([f1]);
+      expect(filterManager.getGlobalFilters()).toHaveLength(0);
+      expect(filterManager.getAppFilters()).toHaveLength(1);
+    });
   });
 
   describe('add filters', () => {
diff --git a/src/plugins/data/public/query/filter_manager/filter_manager.ts b/src/plugins/data/public/query/filter_manager/filter_manager.ts
index 6c5cdbaffce5e..aa77f10d89f63 100644
--- a/src/plugins/data/public/query/filter_manager/filter_manager.ts
+++ b/src/plugins/data/public/query/filter_manager/filter_manager.ts
@@ -124,7 +124,10 @@ export class FilterManager {
 
   /* Setters */
 
-  public addFilters(filters: esFilters.Filter[] | esFilters.Filter, pinFilterStatus?: boolean) {
+  public addFilters(
+    filters: esFilters.Filter[] | esFilters.Filter,
+    pinFilterStatus: boolean = this.uiSettings.get('filters:pinnedByDefault')
+  ) {
     if (!Array.isArray(filters)) {
       filters = [filters];
     }
@@ -133,12 +136,6 @@ export class FilterManager {
       return;
     }
 
-    if (pinFilterStatus === undefined) {
-      pinFilterStatus = this.uiSettings.get('filters:pinnedByDefault');
-    }
-
-    // Set the store of all filters. For now.
-    // In the future, all filters should come in with filter state store already set.
     const store = pinFilterStatus
       ? esFilters.FilterStateStore.GLOBAL_STATE
       : esFilters.FilterStateStore.APP_STATE;
@@ -157,7 +154,16 @@ export class FilterManager {
     this.handleStateUpdate(newFilters);
   }
 
-  public setFilters(newFilters: esFilters.Filter[]) {
+  public setFilters(
+    newFilters: esFilters.Filter[],
+    pinFilterStatus: boolean = this.uiSettings.get('filters:pinnedByDefault')
+  ) {
+    const store = pinFilterStatus
+      ? esFilters.FilterStateStore.GLOBAL_STATE
+      : esFilters.FilterStateStore.APP_STATE;
+
+    FilterManager.setFiltersStore(newFilters, store);
+
     const mappedFilters = mapAndFlattenFilters(newFilters);
     const newPartitionedFilters = FilterManager.partitionFilters(mappedFilters);
     const mergedFilters = this.mergeIncomingFilters(newPartitionedFilters);