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–+ servings
Several chocolate cupcakes with cheesecake centers and chocolate chips, one with a bite taken out of it.
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Meaningful Eats

Gluten-Free Black Bottom Cupcakes

12 cupcakes
These gluten-free black bottom cupcakes feature a rich, fudgy chocolate base with a creamy cheesecake filling baked right into the center. No frosting needed!
The most important thing I learned while testing this recipe: use cold cream cheese straight from the fridge. This helps the filling sink into the center of each cupcake, with just enough peeking through the top to hint at what’s inside!
Course Dessert
Cuisine American
Diet Gluten Free
Prep Time 20 minutes
Cook Time 18 minutes
Total Time 38 minutes

Ingredients

Cream Cheese Filling

  • 8 oz (226g) cream cheese, cold
  • ⅓ cup (66g) granulated sugar
  • 1 large egg, at room temperature
  • pinch of kosher salt
  • ½ cup (90g) mini chocolate chips

Chocolate Cupcake Batter

Instructions

  • Preheat the oven to 350°F. Line a standard muffin pan with paper baking cups.
  • Make the filling: In the bowl of a stand mixer fitted with a paddle attachment, or using a hand mixer, beat the cold cream cheese and sugar on medium-high speed until fully combined and smooth, about 2 minutes. Add the egg and salt and beat again until well-combined, about 2 more minutes. Fold in the mini chocolate chips with a rubber spatula. Set aside.
  • Make the batter: In a large bowl, whisk together the gluten-free flour, sugar, baking soda, cocoa powder, espresso powder (if using) and salt.
  • Add the oil, vinegar, vanilla and hot water. Mix on medium speed for 2–3 minutes, scraping the sides and bottom halfway through, until smooth and fully incorporated. The batter will be thin.
  • Using a kitchen scoop or large spoon, divide the batter evenly among the prepared liners, filling each about halfway. Dollop about 1½ tablespoons of the cream cheese filling into the center of each.
  • Bake for 16–18 minutes, until a toothpick inserted into the chocolate base comes out clean with just a few moist crumbs. The cream cheese should look pale on top — pull them the moment it starts to take on any color.
  • Cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.

Notes

Gluten-Free: Use a gluten-free measure-for-measure flour blend that contains xanthan gum.
Dairy-Free: Dairy-free cream cheese works great here! I really like the brand Violife.
To Make-Ahead: Bake the cupcakes up to 1 day ahead. Once cool, cover and refrigerate until ready to serve. I don't recommend making the batter or filling ahead.
To Store: Leftovers can be stored in an airtight container in the fridge for up to 4 days.
To Freeze: I don't recommend freezing these cupcakes. The cream cheese filling can change texture after freezing and thawing.

Nutrition

Calories: 299kcal | Carbohydrates: 39g | Protein: 4g | Fat: 16g | Saturated Fat: 6g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 6g | Trans Fat: 0.02g | Cholesterol: 34mg | Sodium: 259mg | Potassium: 68mg | Fiber: 2g | Sugar: 28g | Vitamin A: 290IU | Vitamin C: 0.05mg | Calcium: 41mg | Iron: 1mg