Preheat oven to 350°F (175°C) and line a 12-cup muffin tin with paper liners.
Whisk together melted butter and 1 cup sugar. Stir in cocoa powder.
Beat in the 2 eggs one at a time until the batter is glossy. Stir in 1 tsp vanilla.
Gently fold in the flour, salt, and chocolate chips until just combined.
In a separate bowl, beat cream cheese and 1/4 cup sugar until smooth. Mix in the egg yolk and 1/2 tsp vanilla.
Divide brownie batter among muffin cups, reserving 2 tablespoons. Top each with a dollop of cheesecake batter.
Dot the top with reserved brownie batter and swirl with a toothpick.
Bake for 18-22 minutes. Cool in pan, then chill in the refrigerator for at least 2 hours before serving.