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 7857e2989bda65..3f31749ee71f34 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
@@ -170,6 +170,32 @@ describe('filter_manager', () => {
       expect(fetchStub).toBeCalledTimes(0);
       expect(updateStub).toBeCalledTimes(1);
     });
+
+    test('should merge multiple conflicting app filters', async function() {
+      filterManager.addFilters(readyFilters, true);
+      const appFilter1 = _.cloneDeep(readyFilters[1]);
+      appFilter1.meta.negate = true;
+      appFilter1.$state = {
+        store: esFilters.FilterStateStore.APP_STATE,
+      };
+      const appFilter2 = _.cloneDeep(readyFilters[2]);
+      appFilter2.meta.negate = true;
+      appFilter2.$state = {
+        store: esFilters.FilterStateStore.APP_STATE,
+      };
+
+      const globalFilters = filterManager.getFilters();
+      filterManager.setFilters([...globalFilters, appFilter1, appFilter2]);
+
+      // global filters are taking precedence over same app filters when setting
+      const res = filterManager.getFilters();
+      expect(res).toHaveLength(3);
+      expect(
+        res.filter(function(filter) {
+          return filter.$state && filter.$state.store === esFilters.FilterStateStore.GLOBAL_STATE;
+        }).length
+      ).toBe(3);
+    });
   });
 
   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 f7d0dddd5bf039..18bb619f6a1370 100644
--- a/src/plugins/data/public/query/filter_manager/filter_manager.ts
+++ b/src/plugins/data/public/query/filter_manager/filter_manager.ts
@@ -45,20 +45,23 @@ export class FilterManager {
     const appFilters = partitionedFilters.appFilters;
 
     // existing globalFilters should be mutated by appFilters
+    // ignore original appFilters which are already inside globalFilters
+    const cleanedAppFilters: esFilters.Filter[] = [];
     _.each(appFilters, function(filter, i) {
       const match = _.find(globalFilters, function(globalFilter) {
         return compareFilters(globalFilter, filter);
       });
 
-      // no match, do nothing
-      if (!match) return;
+      // no match, do continue with app filter
+      if (!match) {
+        return cleanedAppFilters.push(filter);
+      }
 
-      // matching filter in globalState, update global and remove from appState
+      // matching filter in globalState, update global and don't add from appState
       _.assign(match.meta, filter.meta);
-      appFilters.splice(i, 1);
     });
 
-    return FilterManager.mergeFilters(appFilters, globalFilters);
+    return FilterManager.mergeFilters(cleanedAppFilters, globalFilters);
   }
 
   private static mergeFilters(