diff --git a/public/app/features/dashboard-scene/scene/DashboardControlsMenu.tsx b/public/app/features/dashboard-scene/scene/DashboardControlsMenu.tsx
index d74717c9285..03ac5f0ea88 100644
--- a/public/app/features/dashboard-scene/scene/DashboardControlsMenu.tsx
+++ b/public/app/features/dashboard-scene/scene/DashboardControlsMenu.tsx
@@ -88,7 +88,7 @@ function DashboardControlsMenu({ variables, links, annotationLayers, dashboardUI
     >
       {/* Variables */}
       {variables.map((variable, index) => (
-        <div className={cx({ [styles.variableItem]: index > 0 })} key={variable.state.key}>
+        <div className={cx({ [styles.menuItem]: index > 0 })} key={variable.state.key}>
           <VariableValueSelectWrapper variable={variable} inMenu />
         </div>
       ))}
@@ -96,7 +96,7 @@ function DashboardControlsMenu({ variables, links, annotationLayers, dashboardUI
       {/* Annotation layers */}
       {annotationLayers.length > 0 &&
         annotationLayers.map((layer, index) => (
-          <div className={cx(index > 0 && styles.variableItem)} key={layer.state.key}>
+          <div className={cx({ [styles.menuItem]: variables.length > 0 || index > 0 })} key={layer.state.key}>
             <DataLayerControl layer={layer} inMenu />
           </div>
         ))}
@@ -131,7 +131,7 @@ const getStyles = (theme: GrafanaTheme2) => ({
     marginTop: theme.spacing(2),
     padding: theme.spacing(0, 0.5),
   }),
-  variableItem: css({
+  menuItem: css({
     marginTop: theme.spacing(2),
   }),
 });
diff --git a/public/app/features/dashboard-scene/scene/DataLayerControl.tsx b/public/app/features/dashboard-scene/scene/DataLayerControl.tsx
index 8bc3f2f5c5b..6318fa248a6 100644
--- a/public/app/features/dashboard-scene/scene/DataLayerControl.tsx
+++ b/public/app/features/dashboard-scene/scene/DataLayerControl.tsx
@@ -69,6 +69,8 @@ const getStyles = (theme: GrafanaTheme2) => ({
     '& > div': {
       border: 'none',
       background: 'transparent',
+      paddingRight: theme.spacing(0.5),
+      height: theme.spacing(2),
       '&:hover': {
         border: 'none',
         background: 'transparent',
@@ -76,6 +78,7 @@ const getStyles = (theme: GrafanaTheme2) => ({
     },
   }),
   menuLabel: css({
-    marginTop: theme.spacing(0.5),
+    marginTop: 0,
+    marginBottom: 0,
   }),
 });
diff --git a/public/app/features/dashboard-scene/scene/VariableControls.tsx b/public/app/features/dashboard-scene/scene/VariableControls.tsx
index 470b20fea23..45c48610f1a 100644
--- a/public/app/features/dashboard-scene/scene/VariableControls.tsx
+++ b/public/app/features/dashboard-scene/scene/VariableControls.tsx
@@ -171,10 +171,6 @@ const getStyles = (theme: GrafanaTheme2) => ({
     marginTop: 0,
     marginBottom: 0,
   }),
-  labelWrapper: css({
-    display: 'flex',
-    alignItems: 'center',
-  }),
   labelSelectable: css({
     cursor: 'pointer',
   }),