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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.
5 from 1 vote

Gluten-Free Black Bottom Cupcakes

These gluten-free black bottom cupcakes have a moist chocolate base and a sweet cream cheese center studded with mini chocolate chips baked right in. They have no frosting, which makes them perfect for transporting to parties and potlucks. Ready in under 45 minutes!
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Prep Time 15 minutes
Cook Time 25 minutes
Total Time 40 minutes
Servings 24 cupcakes
Metric - US Customary

Ingredients

For the Cheesecake Filling:

  • 8 oz (226.8 g) cream cheese - softened to room temperature
  • ¼ cup (50 g) granulated sugar
  • 1 (50 g) large egg
  • 1 teaspoon vanilla extract
  • 1 cup (180 g) mini chocolate chips - divided

For the Cupcakes:

  • 3 cups (420 g) gluten-free flour blend - Bob's Red Mill 1-to-1 Gluten-Free Baking Flour (in the blue bag)
  • 2 cups (400 g) brown sugar
  • ⅔ cup (67 g) unsweetened cocoa powder
  • 2 teaspoons espresso powder - optional but recommended
  • 2 teaspoons baking soda
  • 1 teaspoon salt
  • 2 cups (474 g) hot brewed coffee - or boiling water
  • ⅔ cup (132 g) vegetable oil
  • 2 tablespoons (30 g) apple cider vinegar
  • 2 teaspoons vanilla extract

**Use the toggle button above to turn the instruction photos on and off!

Instructions

Make the Cheesecake Filling:

  • Preheat oven to 350°F. Line two 12-cup muffin pans with paper lines (you'll need 24 total). Set aside.
  • In a medium bowl, beat 8 oz (226.8 g) cream cheese with a hand mixer or whisk for 1 minute until smooth and fluffy with no lumps.
  • Add ¼ cup (50 g) granulated sugar, 1 (50 g) large egg, and 1 teaspoon vanilla extract. Beat for 1-2 minutes until completely smooth and combined.
  • Stir in 0.75 cup (135 g) mini chocolate chips¼ cup for topping. Set the bowl aside.

Make the Chocolate Cupcake Batter:

  • In a large bowl, whisk together 3 cups (420 g) gluten-free flour blend, 2 cups (400 g) brown sugar, ⅔ cup (67 g) unsweetened cocoa powder, 2 teaspoons espresso powder, 2 teaspoons baking soda, and 1 teaspoon salt until well combined with no lumps.
    A glass bowl filled with brown sugar, flour, baking powder, and cocoa powder sits on a white towel, surrounded by cupcake liners, a whisk, a measuring cup of flour, and a small container of oil.
  • In a separate bowl or large measuring cup, stir together 2 cups (474 g) hot brewed coffee (or boiling water), ⅔ cup (132 g) vegetable oil, 2 tablespoons (30 g) apple cider vinegar, and 2 teaspoons vanilla extract.
  • Pour the wet ingredients into the dry ingredients and stir until combined and smooth. The batter will be very thin and pourable.
    A glass bowl with dry chocolate cake mix has a well in the center, where brown liquid is being poured in from a glass measuring cup.
  • Divide the chocolate batter evenly among the 24 prepared muffin cups using a cookie scoop, filling each about 2/3 full (about 60-65g of batter per cup)
    A muffin tin filled with cupcake liners, each holding chocolate batter, sits on a marble surface next to a bowl of white batter with chocolate chips and a copper cup filled with mini chocolate chips.
  • Spoon 1 tablespoon of the cheesecake filling onto the center of the chocolate batter in each cup. It will sink slightly, which is normal.
    A close-up of a muffin tin filled with paper liners. Some liners contain chocolate batter, while others have chocolate batter topped with a spoonful of white batter being added.
  • Sprinkle the remaining 0.25 cup (45 g) mini chocolate chips evenly over all 24 cupcakes.
    A muffin tin holds several paper liners filled with chocolate batter and topped with cream cheese mixture and chocolate chips, ready to be baked.
  • Bake at 350°F for 25-27 minutes. The cupcakes are done when the cream cheese topping is lightly golden brown and slightly cracked, and a toothpick inserted into the chocolate portion (not the cheesecake center) comes out clean or with just a few moist crumbs.
    A muffin tin filled with chocolate chip muffins in paper liners, some still unbaked, on a worn baking tray with a white cloth underneath.
  • Remove from the oven and let the cupcakes cool in the pans for 10 minutes. Carefully transfer the cupcakes to a wire rack and let cool completely, at least 30 minutes, before serving. The cheesecake filling needs time to set.

Notes

  • Gluten-Free Flour: I've only tested this recipe with Bob's Red Mill 1-to-1 Gluten Free Baking Flour. Weigh your flour (420g for 3 cups) for the most consistent results. I haven't tested other brands, so I can't guarantee they'll work.
  • Softening Cream Cheese: The cream cheese must be completely softened to room temperature for a smooth filling. If you forgot to take it out ahead of time, keep it in the foil wrapper and submerge it in a bowl of warm water for 5-10 minutes. If your filling has lumps, beat the cream cheese alone for 1-2 minutes until completely smooth before adding the other ingredients.
  • Coffee vs. Water: Hot coffee intensifies the chocolate flavor without making the cupcakes taste like coffee. If you don't drink coffee, use boiling water instead. The cupcakes will still be good, just not quite as chocolatey.
  • Storage: Room temperature in an airtight container for 2-3 days, refrigerate for up to 5 days, or freeze (wrapped individually) for up to 3 months. Thaw at room temperature for 2-3 hours.

Nutrition

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