Black Bottom Cupcakes

published Feb 25, 2022
Black Bottom Cupcakes

A chocolate chip-studded cream cheese filling is what puts these rich chocolate cupcakes over the top.


Prep15 minutes

Cook30 minutes

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cross section of black bottom cupcakes
Credit: Photo: Joe Lingeman; Food Styling: Jesse Szewczyk

Black bottom cupcakes fall somewhere between chocolate cupcakes and cream cheese brownies, which is to say they are positively dreamy. These are cupcakes that eschew frosting. Instead, the tender-crumbed chocolate cake reveals a delicious chocolate chip-studded cream cheese filling when broken apart. They’re a moist, fudgy, and luxuriously rich treat.

What Are Black Bottom Cupcakes Made Of? 

Black bottom cupcakes feature two components: chocolate cake and cream cheese filling.

  • The fluffy chocolate cake is similar to Devil’s food cake and relies on cocoa powder for its chocolate flavor.
  • The cream cheese filling is a simple mix of softened cream cheese, granulated sugar, egg, and vanilla extract. To gild the lily, mini chocolate chips are folded into the filling.

Mini Chocolate Chips vs. Regular Chocolate Chips

Mini chocolate chips are the best choice for the cream cheese filling because they’re light enough to stay suspended in the filling; regular chocolate chips would sink. If you have a bag of regular chips, just use the same amount and give them a rough chop before folding them into the filling.

Should Black Bottom Cupcakes Be Refrigerated?

Because black bottom cupcakes have a cream cheese filling, it’s best to refrigerate them. Pack leftover cupcakes in an airtight container and store them in the fridge for up to 3 days. While you can enjoy them cold, straight from the fridge, I like to leave them out on the counter for 20 minutes or so to come to room temperature before eating.

Credit: Photo: Joe Lingeman; Food Styling: Jesse Szewczyk

Black Bottom Cupcakes

A chocolate chip-studded cream cheese filling is what puts these rich chocolate cupcakes over the top.

Prep time 15 minutes

Cook time 30 minutes

Makes 12

Nutritional Info


  • 8 ounces

    cream cheese

  • 2 teaspoons

    vanilla extract, divided

  • 3/4 plus 1/3 cup

    granulated sugar, divided

  • 2

    large eggs, divided

  • 3/4 teaspoon

    kosher salt, divided

  • 1/2 cup

    mini semisweet chocolate chips

  • 1/2 cup


  • 3/4 cup

    all-purpose flour

  • 1/2 cup

    unsweetened natural cocoa powder (not Dutch-process)

  • 3/4 teaspoon

    baking powder

  • 3/4 teaspoon

    baking soda

  • 1/2 cup

    whole or 2% milk

  • 1/4 cup

    canola or vegetable oil

  • 2 teaspoons

    apple cider or distilled white vinegar


  1. Place 8 ounces cream cheese in the bowl of a stand mixer (or large bowl if using an electric hand mixer). Let sit at room temperature until softened, about 30 minutes. Meanwhile, arrange a rack in the middle of the oven and heat to 350°F. Line a standard 12-well muffin pan with paper liners.

  2. Add 1 teaspoon of the vanilla extract to the cream cheese. Beat with the paddle attachment on medium speed until fluffy, about 1 minute. Scrape down the sides of the bowl and the beater with a rubber spatula. Add 1/3 cup of the granulated sugar, 1 of the large eggs, and 1/4 teaspoon kosher salt. Beat on low speed until combined and mostly smooth (a few lumps are okay), about 1 minute more. Add 1/2 cup mini chocolate chips and beat on low speed until just combined.

  3. Bring 1/2 cup water to a simmer in a small saucepan over medium heat. As soon as the water comes to a simmer, turn the heat off. (Alternatively, use an electric or stovetop tea kettle and bring it to a boil.)

  4. Place 3/4 cup all-purpose flour, the remaining 3/4 cup granulated sugar, 1/2 cup unsweetened cocoa powder, 3/4 teaspoon baking powder, 3/4 teaspoon baking soda, and the remaining 1/2 teaspoon kosher salt in a medium bowl. Whisk to combine.

  5. Add the remaining 1 large egg, 1/2 cup milk, 1/4 cup canola or vegetable oil, 2 teaspoons apple cider or white vinegar, and 1 teaspoon vanilla extract. Whisk to combine. Pour in the hot water and whisk to combine. The batter will be quite thin.

  6. Divide the batter evenly between the wells in the pan, filling each no more than 3/4 full. Dollop each with 2 tablespoons of the cream cheese mixture, dividing it evenly among the cupcakes.

  7. Bake until a toothpick inserted in the center of the cupcakes comes out clean, about 25 minutes. Let the cupcakes cool in the pan for about 10 minutes, then transfer to a wire rack to cool completely.

Recipe Notes

Regular Semisweet Chocolate Chips: 1/2 cup regular-sized semisweet chocolate chips can be used in place of the mini semisweet chocolate chips. Coarsely chop them before adding to the cream cheese mixture.

Storage: Leftover cupcakes can be stored in an airtight container in the refrigerator for up to 3 days.