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A photo of a gluten-free black bottom cupcake with cheesecake filling and topped with mini chocolate chips on a marble table.

Gluten-Free Black Bottom Cupcakes

These gluten-free black bottom cupcakes are filled with a rich chocolate chip cheesecake filling and are perfect for an easy dessert or a fun breakfast treat!
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Course: Dessert
Cuisine: American
Prep Time: 15 minutes
Cook Time: 25 minutes
Total Time: 40 minutes
Servings: 24 cupcakes
Calories: 260kcal
Author: Megan


For the Cheesecake Filling:

  • 8 oz cream cheese (softened)
  • 1 teaspoon vanilla
  • 1 egg
  • 1/4 cup sugar
  • 1 cup mini chocolate chips (divided)

For the Cupcakes:

  • 3 cups gluten free flour blend
  • 1/2 teaspoon xanthan gum (if your blend doesn't already contain it)
  • 2 cups brown sugar
  • 2/3 cup cocoa powder
  • 2 teaspoons espresso powder
  • 2 teaspoons baking soda
  • 1 teaspoon salt
  • 2 cup hot coffee (or boiling water)
  • 2/3 cup vegetable oil
  • 2 tablespoons apple cider vinegar
  • 2 teaspoons vanilla extract


  • Preheat oven to 350F. Line 24 muffin cups with paper liners. Set aside.
  • In a medium bowl, beat together softened cream cheese, vanilla, egg, and sugar, until combined.
  • Stir in 3/4 cup of the mini chocolate chips and set aside.
  • To make the cupcake batter, whisk together the gluten-free flour blend, xanthan gum (if using), brown sugar, cocoa powder, espresso powder, baking soda and salt.
  • In a separate bowl, mix together hot coffee, vegetable oil, apple cider vinegar and vanilla extract.
  • Pour the wet ingredients into the dry ingredients and stir until combined.
  • Portion out the chocolate cupcake batter into each of the 24 muffin liners.
  • Dollop a tablespoon of the cheesecake batter on top of the chocolate cupcake batter.
  • Sprinkle remaining 1/4 cup of mini chocolate chips on top of each cupcake.
  • Bake at 350F for 25-27 minutes, until the tops are lightly browned and a toothpick inserted into the center of each cupcake comes out clean.
  • Let cool completely before serving.


Serving: 24cupcakes | Calories: 260kcal | Carbohydrates: 38g | Protein: 3g | Saturated Fat: 8g | Cholesterol: 18mg | Sodium: 234mg | Fiber: 2g | Sugar: 25g
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