diff --git a/src/legacy/core_plugins/data/public/filter/filter_manager/filter_manager.test.ts b/src/legacy/core_plugins/data/public/filter/filter_manager/filter_manager.test.ts
index 5df1e286fa289..3e264760a148b 100644
--- a/src/legacy/core_plugins/data/public/filter/filter_manager/filter_manager.test.ts
+++ b/src/legacy/core_plugins/data/public/filter/filter_manager/filter_manager.test.ts
@@ -70,7 +70,7 @@ describe('filter_manager', () => {
   let updateListener: sinon.SinonSpy<any[], any>;
 
   let filterManager: FilterManager;
-  let indexPatterns: any;
+  let indexPatterns: StubIndexPatterns;
   let readyFilters: Filter[];
 
   beforeEach(() => {
@@ -440,6 +440,24 @@ describe('filter_manager', () => {
       expect(globalStateStub.filters.length).toBe(3);
     });
 
+    test('should de-dupe globalStateStub filters being set', async () => {
+      const f1 = getFilter(FilterStateStore.GLOBAL_STATE, false, false, 'age', 34);
+      const f2 = _.cloneDeep(f1);
+      await filterManager.setFilters([f1, f2]);
+      expect(filterManager.getAppFilters()).toHaveLength(0);
+      expect(filterManager.getGlobalFilters()).toHaveLength(1);
+      expect(filterManager.getFilters()).toHaveLength(1);
+    });
+
+    test('should de-dupe appStateStub filters being set', async () => {
+      const f1 = getFilter(FilterStateStore.APP_STATE, false, false, 'age', 34);
+      const f2 = _.cloneDeep(f1);
+      await filterManager.setFilters([f1, f2]);
+      expect(filterManager.getAppFilters()).toHaveLength(1);
+      expect(filterManager.getGlobalFilters()).toHaveLength(0);
+      expect(filterManager.getFilters()).toHaveLength(1);
+    });
+
     test('should mutate global filters on appStateStub filter changes', async function() {
       const idx = 1;
       await filterManager.addFilters(readyFilters, true);
diff --git a/src/legacy/core_plugins/data/public/filter/filter_manager/filter_manager.ts b/src/legacy/core_plugins/data/public/filter/filter_manager/filter_manager.ts
index de765c0200365..dfa7bc9c216bc 100644
--- a/src/legacy/core_plugins/data/public/filter/filter_manager/filter_manager.ts
+++ b/src/legacy/core_plugins/data/public/filter/filter_manager/filter_manager.ts
@@ -20,7 +20,7 @@
 import { Filter, isFilterPinned, FilterStateStore } from '@kbn/es-query';
 
 import _ from 'lodash';
-import { Subject, Subscription } from 'rxjs';
+import { Subject } from 'rxjs';
 
 import { npSetup } from 'ui/new_platform';
 
@@ -42,20 +42,13 @@ import { IndexPatterns } from '../../index_patterns';
 export class FilterManager {
   private indexPatterns: IndexPatterns;
   private filters: Filter[] = [];
-  private updated$: Subject<any> = new Subject();
-  private fetch$: Subject<any> = new Subject();
-  private updateSubscription$: Subscription | undefined;
+  private updated$: Subject<void> = new Subject();
+  private fetch$: Subject<void> = new Subject();
 
   constructor(indexPatterns: IndexPatterns) {
     this.indexPatterns = indexPatterns;
   }
 
-  destroy() {
-    if (this.updateSubscription$) {
-      this.updateSubscription$.unsubscribe();
-    }
-  }
-
   private mergeIncomingFilters(partitionedFilters: PartitionedFilters): Filter[] {
     const globalFilters = partitionedFilters.globalFilters;
     const appFilters = partitionedFilters.appFilters;
@@ -74,11 +67,11 @@ export class FilterManager {
       appFilters.splice(i, 1);
     });
 
-    return uniqFilters(appFilters.reverse().concat(globalFilters.reverse())).reverse();
+    return FilterManager.mergeFilters(appFilters, globalFilters);
   }
 
-  private filtersUpdated(newFilters: Filter[]): boolean {
-    return !_.isEqual(this.filters, newFilters);
+  private static mergeFilters(appFilters: Filter[], globalFilters: Filter[]): Filter[] {
+    return uniqFilters(appFilters.reverse().concat(globalFilters.reverse())).reverse();
   }
 
   private static partitionFilters(filters: Filter[]): PartitionedFilters {
@@ -90,9 +83,6 @@ export class FilterManager {
   }
 
   private handleStateUpdate(newFilters: Filter[]) {
-    // This is where the angular update magic \ syncing diget happens
-    const filtersUpdated = this.filtersUpdated(newFilters);
-
     // global filters should always be first
     newFilters.sort(
       (a: Filter, b: Filter): number => {
@@ -106,6 +96,8 @@ export class FilterManager {
       }
     );
 
+    const filtersUpdated = !_.isEqual(this.filters, newFilters);
+
     this.filters = newFilters;
     if (filtersUpdated) {
       this.updated$.next();
@@ -155,24 +147,28 @@ export class FilterManager {
       pinFilterStatus = uiSettings.get('filters:pinnedByDefault');
     }
 
-    // set the store of all filters
-    // TODO: is this necessary?
+    // 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 ? FilterStateStore.GLOBAL_STATE : FilterStateStore.APP_STATE;
     FilterManager.setFiltersStore(filters, store);
 
     const mappedFilters = await mapAndFlattenFilters(this.indexPatterns, filters);
+
+    // This is where we add new filters to the correct place (app \ global)
     const newPartitionedFilters = FilterManager.partitionFilters(mappedFilters);
-    const partitionFilters = this.getPartitionedFilters();
-    partitionFilters.appFilters.push(...newPartitionedFilters.appFilters);
-    partitionFilters.globalFilters.push(...newPartitionedFilters.globalFilters);
+    const currentFilters = this.getPartitionedFilters();
+    currentFilters.appFilters.push(...newPartitionedFilters.appFilters);
+    currentFilters.globalFilters.push(...newPartitionedFilters.globalFilters);
 
-    const newFilters = this.mergeIncomingFilters(partitionFilters);
+    const newFilters = this.mergeIncomingFilters(currentFilters);
     this.handleStateUpdate(newFilters);
   }
 
   public async setFilters(newFilters: Filter[]) {
     const mappedFilters = await mapAndFlattenFilters(this.indexPatterns, newFilters);
-    this.handleStateUpdate(mappedFilters);
+    const newPartitionedFilters = FilterManager.partitionFilters(mappedFilters);
+    const mergedFilters = this.mergeIncomingFilters(newPartitionedFilters);
+    this.handleStateUpdate(mergedFilters);
   }
 
   public removeFilter(filter: Filter) {
diff --git a/src/legacy/core_plugins/data/public/filter/filter_manager/filter_state_manager.ts b/src/legacy/core_plugins/data/public/filter/filter_manager/filter_state_manager.ts
index d9c5af9a6c52f..4fec67df919f4 100644
--- a/src/legacy/core_plugins/data/public/filter/filter_manager/filter_state_manager.ts
+++ b/src/legacy/core_plugins/data/public/filter/filter_manager/filter_state_manager.ts
@@ -25,7 +25,7 @@ import { FilterManager } from './filter_manager';
 
 /**
  * FilterStateManager is responsible for watching for filter changes
- * and synching with FilterManager, as well as syncing FilterManager changes
+ * and syncing with FilterManager, as well as syncing FilterManager changes
  * back to the URL.
  **/
 export class FilterStateManager {