diff --git a/x-pack/legacy/plugins/lens/public/indexpattern_plugin/datapanel.test.tsx b/x-pack/legacy/plugins/lens/public/indexpattern_plugin/datapanel.test.tsx
index 56163d4079f8d..9ff6297c28368 100644
--- a/x-pack/legacy/plugins/lens/public/indexpattern_plugin/datapanel.test.tsx
+++ b/x-pack/legacy/plugins/lens/public/indexpattern_plugin/datapanel.test.tsx
@@ -7,9 +7,9 @@
 import { shallow } from 'enzyme';
 import React, { ChangeEvent, ReactElement } from 'react';
 import { EuiComboBox, EuiFieldSearch, EuiContextMenuPanel } from '@elastic/eui';
-import { IndexPatternPrivateState } from './indexpattern';
+import { IndexPatternPrivateState, IndexPatternColumn } from './indexpattern';
 import { createMockedDragDropContext } from './mocks';
-import { InnerIndexPatternDataPanel } from './datapanel';
+import { InnerIndexPatternDataPanel, IndexPatternDataPanel, MemoizedDataPanel } from './datapanel';
 import { FieldItem } from './field_item';
 import { act } from 'react-dom/test-utils';
 
@@ -205,6 +205,84 @@ describe('IndexPattern Data Panel', () => {
     };
   });
 
+  it('should update index pattern of layer on switch if it is a single empty one', async () => {
+    const setStateSpy = jest.fn();
+    const wrapper = shallow(
+      <IndexPatternDataPanel
+        state={{
+          ...initialState,
+          layers: { first: { indexPatternId: '1', columnOrder: [], columns: {} } },
+        }}
+        setState={setStateSpy}
+        dragDropContext={{ dragging: {}, setDragging: () => {} }}
+      />
+    );
+
+    act(() => {
+      wrapper.find(MemoizedDataPanel).prop('setShowIndexPatternSwitcher')!(true);
+    });
+    wrapper.find(MemoizedDataPanel).prop('onChangeIndexPattern')!('2');
+
+    expect(setStateSpy).toHaveBeenCalledWith({
+      ...initialState,
+      layers: { first: { indexPatternId: '2', columnOrder: [], columns: {} } },
+      currentIndexPatternId: '2',
+    });
+  });
+
+  it('should not update index pattern of layer on switch if there are more than one', async () => {
+    const setStateSpy = jest.fn();
+    const state = {
+      ...initialState,
+      layers: {
+        first: { indexPatternId: '1', columnOrder: [], columns: {} },
+        second: { indexPatternId: '1', columnOrder: [], columns: {} },
+      },
+    };
+    const wrapper = shallow(
+      <IndexPatternDataPanel
+        state={state}
+        setState={setStateSpy}
+        dragDropContext={{ dragging: {}, setDragging: () => {} }}
+      />
+    );
+
+    act(() => {
+      wrapper.find(MemoizedDataPanel).prop('setShowIndexPatternSwitcher')!(true);
+    });
+    wrapper.find(MemoizedDataPanel).prop('onChangeIndexPattern')!('2');
+
+    expect(setStateSpy).toHaveBeenCalledWith({ ...state, currentIndexPatternId: '2' });
+  });
+
+  it('should not update index pattern of layer on switch if there are columns configured', async () => {
+    const setStateSpy = jest.fn();
+    const state = {
+      ...initialState,
+      layers: {
+        first: {
+          indexPatternId: '1',
+          columnOrder: ['col1'],
+          columns: { col1: {} as IndexPatternColumn },
+        },
+      },
+    };
+    const wrapper = shallow(
+      <IndexPatternDataPanel
+        state={state}
+        setState={setStateSpy}
+        dragDropContext={{ dragging: {}, setDragging: () => {} }}
+      />
+    );
+
+    act(() => {
+      wrapper.find(MemoizedDataPanel).prop('setShowIndexPatternSwitcher')!(true);
+    });
+    wrapper.find(MemoizedDataPanel).prop('onChangeIndexPattern')!('2');
+
+    expect(setStateSpy).toHaveBeenCalledWith({ ...state, currentIndexPatternId: '2' });
+  });
+
   it('should render a warning if there are no index patterns', () => {
     const wrapper = shallow(
       <InnerIndexPatternDataPanel {...defaultProps} currentIndexPatternId="" indexPatterns={{}} />
diff --git a/x-pack/legacy/plugins/lens/public/indexpattern_plugin/datapanel.tsx b/x-pack/legacy/plugins/lens/public/indexpattern_plugin/datapanel.tsx
index ccc8ff6f83cec..74c19ad2cf0e3 100644
--- a/x-pack/legacy/plugins/lens/public/indexpattern_plugin/datapanel.tsx
+++ b/x-pack/legacy/plugins/lens/public/indexpattern_plugin/datapanel.tsx
@@ -4,7 +4,7 @@
  * you may not use this file except in compliance with the Elastic License.
  */
 
-import _ from 'lodash';
+import { mapValues, uniq } from 'lodash';
 import React, { useState, useEffect, memo, useCallback } from 'react';
 import {
   EuiComboBox,
@@ -30,6 +30,7 @@ import { IndexPatternPrivateState, IndexPatternField, IndexPattern } from './ind
 import { ChildDragDropProvider, DragContextState } from '../drag_drop';
 import { FieldItem } from './field_item';
 import { FieldIcon } from './field_icon';
+import { updateLayerIndexPattern } from './state_helpers';
 
 // TODO the typings for EuiContextMenuPanel are incorrect - watchedItemProps is missing. This can be removed when the types are adjusted
 const FixedEuiContextMenuPanel = (EuiContextMenuPanel as unknown) as React.FunctionComponent<
@@ -50,6 +51,11 @@ const fieldTypeNames: Record<DataType, string> = {
   date: i18n.translate('xpack.lens.datatypes.date', { defaultMessage: 'date' }),
 };
 
+function isSingleEmptyLayer(layerMap: IndexPatternPrivateState['layers']) {
+  const layers = Object.values(layerMap);
+  return layers.length === 1 && layers[0].columnOrder.length === 0;
+}
+
 export function IndexPatternDataPanel({
   setState,
   state,
@@ -62,6 +68,11 @@ export function IndexPatternDataPanel({
     (newIndexPattern: string) => {
       setState({
         ...state,
+        layers: isSingleEmptyLayer(state.layers)
+          ? mapValues(state.layers, layer =>
+              updateLayerIndexPattern(layer, indexPatterns[newIndexPattern])
+            )
+          : state.layers,
         currentIndexPatternId: newIndexPattern,
       });
     },
@@ -160,7 +171,7 @@ export const InnerIndexPatternDataPanel = function InnerIndexPatternDataPanel({
     )
     .slice(0, pageSize);
 
-  const availableFieldTypes = _.uniq(filteredFields.map(({ type }) => type));
+  const availableFieldTypes = uniq(filteredFields.map(({ type }) => type));
   const availableFilteredTypes = state.typeFilter.filter(type =>
     availableFieldTypes.includes(type)
   );