Preheat oven to 350 F. In a large bowl, whisk together flour, sugar, cocoa powder, salt, and baking powder. Add in eggs, melted butter, and vanilla extract. Whisk until smooth.
In a large bowl using a mixer, beat softened cream cheese, sugar, egg, and vanilla extract. Beat until smooth. Evenly divide brownie batter between 12 greased muffin cups.
Add the cheesecake filling on top of the brownie batter, swirl with a knife. Bake for 12-15 minutes.