Preheat the oven to 375°F (190°C) and line a 12-cup muffin pan with paper liners.
Whisk together the flour, baking powder, baking soda, salt, and cinnamon.
In another bowl, whisk the granulated sugar, brown sugar, melted butter, eggs, vanilla, and milk.
Fold the wet ingredients into the dry ingredients until just combined.
Beat the cream cheese with sugar and vanilla until smooth.
Fill each muffin cup halfway with batter.
Spoon about one tablespoon of cream cheese filling into the center of each muffin.
Cover the filling with additional muffin batter until cups are about three-quarters full.
Mix the cinnamon and sugar for the topping.
Brush the tops lightly with melted butter.
Sprinkle the cinnamon sugar evenly over each muffin.
Bake for 20–22 minutes or until the tops are golden and a toothpick inserted into the muffin portion comes out clean.
Cool in the pan for 5 minutes before transferring to a wire rack.
Serve warm or at room temperature.