In a mixing bowl, combine flour, brown sugar, cocoa powder, baking soda, and salt. In another mixing bowl, combine cream cheese, peanut butter, honey, remaining milk, and vanilla extract. Place 2 tablespoons batter into prepared cups. Spoon rounded teaspoon of cream cheese mixture into center of each.
Fill cups half full with remaining batter, one tablespoon each.
Bake for 20 minutes.