diff --git a/public/app/features/dashboard-scene/serialization/sceneVariablesSetToVariables.test.ts b/public/app/features/dashboard-scene/serialization/sceneVariablesSetToVariables.test.ts
index f45193f2ad8..33f06a7accc 100644
--- a/public/app/features/dashboard-scene/serialization/sceneVariablesSetToVariables.test.ts
+++ b/public/app/features/dashboard-scene/serialization/sceneVariablesSetToVariables.test.ts
@@ -380,6 +380,35 @@ describe('sceneVariablesSetToVariables', () => {
     `);
   });
 
+  it('should handle Custom variable when sceneVariablesSetToVariables should keep options', () => {
+    const variable = new CustomVariable({
+      name: 'test',
+      label: 'test-label',
+      description: 'test-desc',
+      hide: VariableHide.inControlsMenu,
+      value: ['test'],
+      text: ['test'],
+      query: 'test,test1,test2',
+      options: [
+        { label: 'test', value: 'test' },
+        { label: 'test1', value: 'test1' },
+        { label: 'test2', value: 'test2' },
+      ],
+      includeAll: true,
+      allValue: 'test-all',
+      isMulti: true,
+    });
+
+    const set = new SceneVariableSet({
+      variables: [variable],
+    });
+    const keepQueryOptions = true;
+    const result = sceneVariablesSetToVariables(set, keepQueryOptions);
+    expect(result).toHaveLength(1);
+    expect(result[0].options).not.toEqual([]);
+    expect(result[0].options?.length).toEqual(3);
+  });
+
   it('should handle ConstantVariable', () => {
     const variable = new ConstantVariable({
       name: 'test',
diff --git a/public/app/features/dashboard-scene/serialization/sceneVariablesSetToVariables.ts b/public/app/features/dashboard-scene/serialization/sceneVariablesSetToVariables.ts
index 466d659ab4b..4fad1e3b317 100644
--- a/public/app/features/dashboard-scene/serialization/sceneVariablesSetToVariables.ts
+++ b/public/app/features/dashboard-scene/serialization/sceneVariablesSetToVariables.ts
@@ -102,6 +102,10 @@ export function sceneVariablesSetToVariables(set: SceneVariables, keepQueryOptio
       }
       variables.push(variableObj);
     } else if (sceneUtils.isCustomVariable(variable)) {
+      let options: VariableOption[] = [];
+      if (keepQueryOptions) {
+        options = variableValueOptionsToVariableOptions(variable.state);
+      }
       const customVariable: VariableModel = {
         ...commonProperties,
         current: {
@@ -110,7 +114,7 @@ export function sceneVariablesSetToVariables(set: SceneVariables, keepQueryOptio
           // @ts-expect-error
           value: variable.state.value,
         },
-        options: [],
+        options,
         query: variable.state.query,
         multi: variable.state.isMulti,
         allValue: variable.state.allValue,