Preheat oven to 350°F. Line a 12-cup muffin pan with paper liners.
Beat cream cheese and butter on high until fluffy, about 4 minutes. Add in half of the chopped cherries, powdered sugar, and ½ tsp. vanilla, and beat until smooth. Set aside.
In a large mixing bowl, whisk together flour, baking powder, and baking soda.
In a separate mixing bowl, whisk together milk, egg whites, brown sugar, oil, and 1 ½ tsp. vanilla until brown sugar has dissolved. Stir in dry ingredients until well combined. Fold in remaining chopped cherries.
Divide batter evenly into lined muffin pan, filling about half full.
Bake for 14-16 minutes.
Cool completely, then frost.