diff --git a/cypress/integration/edit.js b/cypress/integration/edit.js
index c16a2fac369..64a882113fb 100644
--- a/cypress/integration/edit.js
+++ b/cypress/integration/edit.js
@@ -68,6 +68,41 @@ describe('Edit Page', () => {
                 expect(el).to.have.value(date)
             );
         });
+
+        it('should change reference list correctly when changing filter', () => {
+            const EditPostTagsPage = editPageFactory('/#/posts/13');
+            EditPostTagsPage.navigate();
+            EditPostTagsPage.gotoTab(3);
+
+            // Music is selected by default
+            cy.get(
+                EditPostTagsPage.elements.input('tags', 'reference-array-input')
+            )
+                .get(`div[role=button]`)
+                .contains('Music')
+                .should('exist');
+
+            EditPostTagsPage.clickInput('change-filter');
+
+            // Music should not be selected anymore after filter reset
+            cy.get(
+                EditPostTagsPage.elements.input('tags', 'reference-array-input')
+            )
+                .get(`div[role=button]`)
+                .contains('Music')
+                .should('not.exist');
+
+            EditPostTagsPage.clickInput('tags', 'reference-array-input');
+
+            // Music should not be visible in the list after filter reset
+            cy.get('div[role=listbox]')
+                .contains('Music')
+                .should('not.exist');
+
+            cy.get('div[role=listbox]')
+                .contains('Photo')
+                .should('exist');
+        });
     });
 
     it('should fill form correctly even when switching from one form type to another', () => {
diff --git a/cypress/support/EditPage.js b/cypress/support/EditPage.js
index 61c896d106c..c6084bfed06 100644
--- a/cypress/support/EditPage.js
+++ b/cypress/support/EditPage.js
@@ -6,6 +6,9 @@ export default url => ({
             if (type === 'rich-text-input') {
                 return `.ra-input-${name} .ql-editor`;
             }
+            if (type === 'reference-array-input') {
+                return `.ra-input div[role=combobox]`;
+            }
             return `.edit-page [name='${name}']`;
         },
         inputs: `.ra-input`,
@@ -37,8 +40,8 @@ export default url => ({
         }
     },
 
-    clickInput(name) {
-        cy.get(this.elements.input(name)).click();
+    clickInput(name, type = 'input') {
+        cy.get(this.elements.input(name, type)).click();
     },
 
     gotoTab(index) {
diff --git a/examples/simple/src/posts/PostEdit.js b/examples/simple/src/posts/PostEdit.js
index c97042246b9..7350e37e0fe 100644
--- a/examples/simple/src/posts/PostEdit.js
+++ b/examples/simple/src/posts/PostEdit.js
@@ -2,7 +2,6 @@ import RichTextInput from 'ra-input-rich-text';
 import React from 'react';
 import {
     TopToolbar,
-    AutocompleteArrayInput,
     AutocompleteInput,
     ArrayInput,
     BooleanInput,
@@ -18,7 +17,6 @@ import {
     ImageField,
     ImageInput,
     NumberInput,
-    ReferenceArrayInput,
     ReferenceManyField,
     ReferenceInput,
     SelectInput,
@@ -32,6 +30,7 @@ import {
     FormDataConsumer,
 } from 'react-admin'; // eslint-disable-line import/no-unresolved
 import PostTitle from './PostTitle';
+import TagReferenceInput from './TagReferenceInput';
 
 const EditActions = ({ basePath, data, hasShow }) => (
     <TopToolbar>
@@ -121,13 +120,11 @@ const PostEdit = ({ permissions, ...props }) => (
                 />
             </FormTab>
             <FormTab label="post.form.miscellaneous">
-                <ReferenceArrayInput
+                <TagReferenceInput
                     reference="tags"
                     source="tags"
-                    filter={{ published: true }}
-                >
-                    <AutocompleteArrayInput fullWidth />
-                </ReferenceArrayInput>
+                    label="Tags"
+                />
                 <ArrayInput source="backlinks">
                     <SimpleFormIterator>
                         <DateInput source="date" />
diff --git a/examples/simple/src/posts/TagReferenceInput.js b/examples/simple/src/posts/TagReferenceInput.js
new file mode 100644
index 00000000000..f529879ac90
--- /dev/null
+++ b/examples/simple/src/posts/TagReferenceInput.js
@@ -0,0 +1,46 @@
+import React, { useState } from 'react';
+import { useForm } from 'react-final-form';
+import { AutocompleteArrayInput, ReferenceArrayInput } from 'react-admin';
+import Button from '@material-ui/core/Button';
+import { makeStyles } from '@material-ui/core/styles';
+
+const useStyles = makeStyles({
+    button: {
+        margin: '0 24px',
+        position: 'relative',
+    },
+    input: {
+        display: 'flex',
+        flexDirection: 'row',
+        justifyContent: 'flex-start',
+        width: '50%',
+    },
+});
+
+const TagReferenceInput = ({ ...props }) => {
+    const classes = useStyles();
+    const { change } = useForm();
+    const [filter, setFilter] = useState(true);
+
+    const handleAddFilter = () => {
+        setFilter(!filter);
+        change('tags', []);
+    };
+
+    return (
+        <div className={classes.input}>
+            <ReferenceArrayInput {...props} filter={{ published: filter }}>
+                <AutocompleteArrayInput />
+            </ReferenceArrayInput>
+            <Button
+                name="change-filter"
+                className={classes.button}
+                onClick={handleAddFilter}
+            >
+                Filter {filter ? 'Unpublished' : 'Published'} Tags
+            </Button>
+        </div>
+    );
+};
+
+export default TagReferenceInput;
diff --git a/packages/ra-core/src/controller/input/ReferenceArrayInputController.spec.tsx b/packages/ra-core/src/controller/input/ReferenceArrayInputController.spec.tsx
index d7b4d6e56d0..2b38056cadf 100644
--- a/packages/ra-core/src/controller/input/ReferenceArrayInputController.spec.tsx
+++ b/packages/ra-core/src/controller/input/ReferenceArrayInputController.spec.tsx
@@ -27,7 +27,8 @@ describe('<ReferenceArrayInputController />', () => {
                 input={{ value: [1, 2] }}
             >
                 {children}
-            </ReferenceArrayInputController>
+            </ReferenceArrayInputController>,
+            { admin: { resources: { tags: { data: {} } } } }
         );
 
         expect(queryByText('true')).not.toBeNull();
@@ -43,7 +44,8 @@ describe('<ReferenceArrayInputController />', () => {
                 input={{ value: [1, 2] }}
             >
                 {children}
-            </ReferenceArrayInputController>
+            </ReferenceArrayInputController>,
+            { admin: { resources: { tags: { data: {} } } } }
         );
         expect(queryByText('true')).not.toBeNull();
     });
@@ -110,6 +112,7 @@ describe('<ReferenceArrayInputController />', () => {
             </ReferenceArrayInputController>,
             {
                 admin: {
+                    resources: { tags: { data: {} } },
                     references: {
                         possibleValues: {
                             'posts@tag_ids': { error: 'boom' },
@@ -234,6 +237,7 @@ describe('<ReferenceArrayInputController />', () => {
             </ReferenceArrayInputController>,
             {
                 admin: {
+                    resources: { tags: { data: { 5: {}, 6: {} } } },
                     references: {
                         possibleValues: {
                             'posts@tag_ids': [],
@@ -288,7 +292,8 @@ describe('<ReferenceArrayInputController />', () => {
         const { dispatch } = renderWithRedux(
             <ReferenceArrayInputController {...defaultProps} allowEmpty>
                 {children}
-            </ReferenceArrayInputController>
+            </ReferenceArrayInputController>,
+            { admin: { resources: { tags: { data: {} } } } }
         );
         expect(dispatch.mock.calls[0][0]).toEqual({
             type: CRUD_GET_MATCHING,
@@ -425,7 +430,8 @@ describe('<ReferenceArrayInputController />', () => {
                 input={{ value: [5, 6] }}
             >
                 {children}
-            </ReferenceArrayInputController>
+            </ReferenceArrayInputController>,
+            { admin: { resources: { tags: { data: { 5: {}, 6: {} } } } } }
         );
         await wait(() => {
             expect(dispatch).toHaveBeenCalledWith({
@@ -449,7 +455,8 @@ describe('<ReferenceArrayInputController />', () => {
                 input={{ value: [5] }}
             >
                 {children}
-            </ReferenceArrayInputController>
+            </ReferenceArrayInputController>,
+            { admin: { resources: { tags: { data: { 5: {} } } } } }
         );
 
         fireEvent.click(getByLabelText('Filter'));
@@ -477,7 +484,8 @@ describe('<ReferenceArrayInputController />', () => {
                 input={{ value: [5] }}
             >
                 {children}
-            </ReferenceArrayInputController>
+            </ReferenceArrayInputController>,
+            { admin: { resources: { tags: { data: { 5: {} } } } } }
         );
 
         rerender(
@@ -614,9 +622,9 @@ describe('<ReferenceArrayInputController />', () => {
                 input={{ value: [5, 6] }}
             >
                 {children}
-            </ReferenceArrayInputController>
+            </ReferenceArrayInputController>,
+            { admin: { resources: { tags: { data: { 5: {}, 6: {} } } } } }
         );
-
         await wait();
         expect(dispatch).toHaveBeenCalledWith({
             type: CRUD_GET_MANY,
diff --git a/packages/ra-core/src/controller/input/useReferenceArrayInputController.ts b/packages/ra-core/src/controller/input/useReferenceArrayInputController.ts
index e8da163c4f3..0aabe0c8b10 100644
--- a/packages/ra-core/src/controller/input/useReferenceArrayInputController.ts
+++ b/packages/ra-core/src/controller/input/useReferenceArrayInputController.ts
@@ -56,13 +56,43 @@ const useReferenceArrayInputController = ({
     // optimization: we fetch selected items only once. When the user selects more items,
     // as we already have the past selected items in the store, we don't fetch them.
     useEffect(() => {
+        // Only fetch new ids
         const newIdsToFetch = difference(input.value, inputValue.current);
-        if (newIdsToFetch.length > 0) {
+        // Only get from store ids selected and already fetched
+        const newIdsToGetFromStore = difference(input.value, newIdsToFetch);
+        /*
+            input.value (current)
+                +------------------------+
+                | ********************** |
+                | ********************** |  inputValue.current (old)
+                | ********** +-----------------------+
+                | ********** | ooooooooo |           |
+                | ********** | ooooooooo |           |
+                | ********** | ooooooooo |           |
+                | ********** | ooooooooo |           |
+                +---|--------|------|----+           |
+                    |        |      |                |
+                    |        |      |                |
+                    |        +------|----------------+
+                    |               |
+            newIdsToFetch    newIdsToGetFromStore
+        */
+        // Change states each time input values changes to avoid keeping previous values no more selected
+        if (!isEqual(idsToFetch, newIdsToFetch)) {
             setIdsToFetch(newIdsToFetch);
-            setIdsToGetFromStore(inputValue.current || []);
         }
+        if (!isEqual(idsToGetFromStore, newIdsToGetFromStore)) {
+            setIdsToGetFromStore(newIdsToGetFromStore);
+        }
+
         inputValue.current = input.value;
-    }, [input.value, setIdsToFetch]);
+    }, [
+        idsToFetch,
+        idsToGetFromStore,
+        input.value,
+        setIdsToFetch,
+        setIdsToGetFromStore,
+    ]);
 
     const [pagination, setPagination] = useState({ page: 1, perPage });
     const [sort, setSort] = useState(defaultSort);