diff --git a/src/legacy/core_plugins/kibana/migrations.js b/src/legacy/core_plugins/kibana/migrations.js
index 744671dbbe8fd..2eb418660f7ab 100644
--- a/src/legacy/core_plugins/kibana/migrations.js
+++ b/src/legacy/core_plugins/kibana/migrations.js
@@ -78,6 +78,33 @@ export const migrations = {
         delete doc.attributes.savedSearchId;
       }
 
+      // Migrate controls
+      const visStateJSON = get(doc, 'attributes.visState');
+      if (visStateJSON) {
+        let visState;
+        try {
+          visState = JSON.parse(visStateJSON);
+        } catch (e) {
+          // Let it go, the data is invalid and we'll leave it as is
+        }
+        if (visState) {
+          const controls = get(visState, 'params.controls') || [];
+          controls.forEach((control, i) => {
+            if (!control.indexPattern) {
+              return;
+            }
+            control.indexPatternRefName = `control_${i}_index_pattern`;
+            doc.references.push({
+              name: control.indexPatternRefName,
+              type: 'index-pattern',
+              id: control.indexPattern,
+            });
+            delete control.indexPattern;
+          });
+          doc.attributes.visState = JSON.stringify(visState);
+        }
+      }
+
       // Migrate table splits
       try {
         const visState = JSON.parse(doc.attributes.visState);
diff --git a/src/legacy/core_plugins/kibana/migrations.test.js b/src/legacy/core_plugins/kibana/migrations.test.js
index f7f62807afd51..f06e6e327f83c 100644
--- a/src/legacy/core_plugins/kibana/migrations.test.js
+++ b/src/legacy/core_plugins/kibana/migrations.test.js
@@ -313,6 +313,50 @@ Object {
       /* eslint-enable max-len */
     });
 
+    it('extracts index patterns from controls', () => {
+      const doc = {
+        id: '1',
+        type: 'visualization',
+        attributes: {
+          foo: true,
+          visState: JSON.stringify({
+            bar: false,
+            params: {
+              controls: [
+                {
+                  bar: true,
+                  indexPattern: 'pattern*',
+                },
+                {
+                  foo: true,
+                },
+              ],
+            },
+          }),
+        },
+      };
+      const migratedDoc = migrate(doc);
+      /* eslint-disable max-len */
+      expect(migratedDoc).toMatchInlineSnapshot(`
+Object {
+  "attributes": Object {
+    "foo": true,
+    "visState": "{\\"bar\\":false,\\"params\\":{\\"controls\\":[{\\"bar\\":true,\\"indexPatternRefName\\":\\"control_0_index_pattern\\"},{\\"foo\\":true}]}}",
+  },
+  "id": "1",
+  "references": Array [
+    Object {
+      "id": "pattern*",
+      "name": "control_0_index_pattern",
+      "type": "index-pattern",
+    },
+  ],
+  "type": "visualization",
+}
+`);
+    /* eslint-enable max-len */
+    });
+
     it('skips extracting savedSearchId when missing', () => {
       const doc = {
         id: '1',
@@ -1157,7 +1201,7 @@ Object {
   "type": "search",
 }
 `);
-    /* eslint-enable max-len */
+      /* eslint-enable max-len */
     });
   });
 });
diff --git a/src/legacy/core_plugins/kibana/public/visualize/saved_visualizations/saved_visualization_references.js b/src/legacy/core_plugins/kibana/public/visualize/saved_visualizations/saved_visualization_references.js
index 953c32e58e1b7..2e2a9eb5d0661 100644
--- a/src/legacy/core_plugins/kibana/public/visualize/saved_visualizations/saved_visualization_references.js
+++ b/src/legacy/core_plugins/kibana/public/visualize/saved_visualizations/saved_visualization_references.js
@@ -18,34 +18,66 @@
  */
 
 export function extractReferences({ attributes, references = [] }) {
-  if (!attributes.savedSearchId) {
-    return { attributes, references };
+  const updatedAttributes = { ...attributes };
+  const updatedReferences = [...references];
+
+  // Extract saved search
+  if (updatedAttributes.savedSearchId) {
+    updatedReferences.push({
+      name: 'search_0',
+      type: 'search',
+      id: updatedAttributes.savedSearchId,
+    });
+    delete updatedAttributes.savedSearchId;
+    updatedAttributes.savedSearchRefName = 'search_0';
+  }
+
+  // Extract index patterns from controls
+  if (updatedAttributes.visState) {
+    const visState = JSON.parse(updatedAttributes.visState);
+    const controls = visState.params && visState.params.controls || [];
+    controls.forEach((control, i) => {
+      if (!control.indexPattern) {
+        return;
+      }
+      control.indexPatternRefName = `control_${i}_index_pattern`;
+      updatedReferences.push({
+        name: control.indexPatternRefName,
+        type: 'index-pattern',
+        id: control.indexPattern,
+      });
+      delete control.indexPattern;
+    });
+    updatedAttributes.visState = JSON.stringify(visState);
   }
+
   return {
-    references: [
-      ...references,
-      {
-        type: 'search',
-        name: 'search_0',
-        id: attributes.savedSearchId,
-      },
-    ],
-    attributes: {
-      ...attributes,
-      savedSearchId: undefined,
-      savedSearchRefName: 'search_0',
-    },
+    references: updatedReferences,
+    attributes: updatedAttributes,
   };
 }
 
 export function injectReferences(savedObject, references) {
-  if (!savedObject.savedSearchRefName) {
-    return;
+  if (savedObject.savedSearchRefName) {
+    const savedSearchReference = references.find(reference => reference.name === savedObject.savedSearchRefName);
+    if (!savedSearchReference) {
+      throw new Error(`Could not find saved search reference "${savedObject.savedSearchRefName}"`);
+    }
+    savedObject.savedSearchId = savedSearchReference.id;
+    delete savedObject.savedSearchRefName;
   }
-  const reference = references.find(reference => reference.name === savedObject.savedSearchRefName);
-  if (!reference) {
-    throw new Error(`Could not find reference "${savedObject.savedSearchRefName}"`);
+  if (savedObject.visState) {
+    const controls = (savedObject.visState.params && savedObject.visState.params.controls) || [];
+    controls.forEach((control) => {
+      if (!control.indexPatternRefName) {
+        return;
+      }
+      const reference = references.find(reference => reference.name === control.indexPatternRefName);
+      if (!reference) {
+        throw new Error (`Could not find index pattern reference "${control.indexPatternRefName}"`);
+      }
+      control.indexPattern = reference.id;
+      delete control.indexPatternRefName;
+    });
   }
-  savedObject.savedSearchId = reference.id;
-  delete savedObject.savedSearchRefName;
 }
diff --git a/src/legacy/core_plugins/kibana/public/visualize/saved_visualizations/saved_visualization_references.test.js b/src/legacy/core_plugins/kibana/public/visualize/saved_visualizations/saved_visualization_references.test.js
index be9375dc33e56..df17e9c1bb30a 100644
--- a/src/legacy/core_plugins/kibana/public/visualize/saved_visualizations/saved_visualization_references.test.js
+++ b/src/legacy/core_plugins/kibana/public/visualize/saved_visualizations/saved_visualization_references.test.js
@@ -51,7 +51,6 @@ Object {
 Object {
   "attributes": Object {
     "foo": true,
-    "savedSearchId": undefined,
     "savedSearchRefName": "search_0",
   },
   "references": Array [
@@ -64,6 +63,46 @@ Object {
 }
 `);
   });
+
+  test('extracts references from controls', () => {
+    const doc = {
+      id: '1',
+      attributes: {
+        foo: true,
+        visState: JSON.stringify({
+          params: {
+            controls: [
+              {
+                bar: true,
+                indexPattern: 'pattern*',
+              },
+              {
+                bar: false,
+              },
+            ],
+          },
+        }),
+      },
+    };
+    const updatedDoc = extractReferences(doc);
+    /* eslint-disable max-len */
+    expect(updatedDoc).toMatchInlineSnapshot(`
+Object {
+  "attributes": Object {
+    "foo": true,
+    "visState": "{\\"params\\":{\\"controls\\":[{\\"bar\\":true,\\"indexPatternRefName\\":\\"control_0_index_pattern\\"},{\\"bar\\":false}]}}",
+  },
+  "references": Array [
+    Object {
+      "id": "pattern*",
+      "name": "control_0_index_pattern",
+      "type": "index-pattern",
+    },
+  ],
+}
+`);
+  /* eslint-enable max-len */
+  });
 });
 
 describe('injectReferences', () => {
@@ -86,6 +125,19 @@ Object {
       id: '1',
       foo: true,
       savedSearchRefName: 'search_0',
+      visState: {
+        params: {
+          controls: [
+            {
+              foo: true,
+              indexPatternRefName: 'control_0_index_pattern',
+            },
+            {
+              foo: false,
+            },
+          ],
+        },
+      },
     };
     const references = [
       {
@@ -93,6 +145,11 @@ Object {
         type: 'search',
         id: '123',
       },
+      {
+        name: 'control_0_index_pattern',
+        type: 'index-pattern',
+        id: 'pattern*',
+      },
     ];
     injectReferences(context, references);
     expect(context).toMatchInlineSnapshot(`
@@ -100,18 +157,50 @@ Object {
   "foo": true,
   "id": "1",
   "savedSearchId": "123",
+  "visState": Object {
+    "params": Object {
+      "controls": Array [
+        Object {
+          "foo": true,
+          "indexPattern": "pattern*",
+        },
+        Object {
+          "foo": false,
+        },
+      ],
+    },
+  },
 }
 `);
   });
 
-  test(`fails when it can't find the reference in the array`, () => {
+  test(`fails when it can't find the saved search reference in the array`, () => {
     const context = {
       id: '1',
       foo: true,
       savedSearchRefName: 'search_0',
     };
     expect(() => injectReferences(context, [])).toThrowErrorMatchingInlineSnapshot(
-      `"Could not find reference \\"search_0\\""`
+      `"Could not find saved search reference \\"search_0\\""`
+    );
+  });
+
+  test(`fails when it can't find the index pattern reference in the array`, () => {
+    const context = {
+      id: '1',
+      visState: {
+        params: {
+          controls: [
+            {
+              foo: true,
+              indexPatternRefName: 'control_0_index_pattern',
+            },
+          ],
+        },
+      },
+    };
+    expect(() => injectReferences(context, [])).toThrowErrorMatchingInlineSnapshot(
+      `"Could not find index pattern reference \\"control_0_index_pattern\\""`
     );
   });
 });