Preparation Steps

• Line a 12-cup muffin pan with paper liners and heat the oven to 350°F (177°C).
• Bloom the chocolate: Warm the milk until steaming (not boiling), then whisk in the cocoa powder and espresso powder until smooth and glossy. Let cool 5 minutes.
• Make the cheesecake swirl: In a medium bowl, beat the cream cheese and 1/4 cup sugar until creamy. Mix in the egg, vanilla, and lemon zest until silky, then fold in the mini chips. Refrigerate 10 minutes to slightly thicken.
• Whisk the dry cupcake ingredients (flour, 3/4 cup sugar, baking soda, and salt) in a large bowl. In a separate bowl, whisk the egg, oil, and vanilla. Stream the warm cocoa-milk mixture into the egg mixture, then pour the liquids over the dry ingredients and whisk just until smooth. Let the batter rest for 5 minutes.
• Portion and par-bake: Divide the chocolate batter among liners, filling just under halfway (about 2 tablespoons each). Bake for 4 minutes to lightly set the bottoms.
• Top and finish: Remove the pan from the oven and spoon about 1 1/2 tablespoons of cheesecake mixture onto the center of each cupcake. If you like, drag a toothpick once through the cheesecake to nudge it toward the edges. Return to the oven and bake 14 to 17 minutes, until a toothpick inserted into the chocolate portion comes out clean and the cheesecake looks set at the edges with a slight wobble in the center.
• Cool in the pan for 5 minutes, transfer to a rack to cool completely, then chill at least 1 hour for the cleanest layers. Store covered in the refrigerator and serve slightly cool or at room temperature.