Gluten-Free Black Bottom Cupcakes

These gluten-free black bottom cupcakes are rich chocolate cupcakes with a chocolate chip cheesecake center and no frosting. The chocolate base is made with oil and coffee, which keeps it moist and intensifies the chocolate flavor. The cream cheese topping is sweetened and loaded with mini chocolate chips.

When you bake them, the chocolate batter sinks to the bottom and the cream cheese filling sits on top, which is how they get the name “black bottom.”

Why You’ll Love this Recipe

• Chocolate and cheesecake in one bite . The chocolate cupcake is rich and moist, and the cream cheese filling is sweet and creamy with little pockets of melted chocolate chips throughout.
• Easy to transport . No frosting means you can stack them in a container without worrying about ruined cupcakes. I’ve brought these to so many parties and they always arrive looking perfect.
• Nobody knows they’re gluten-free. I’ve served these to so many people who don’t eat gluten-free, and the response is always the same: “Wait, these are gluten-free?”

Ingredient Notes

• Gluten-Free Flour Blend: I use Bob’s Red Mill 1-to-1 Gluten Free Baking Flour. This is the only brand I’ve tested in this recipe. Weigh your flour (420g for 3 cups) for the most consistent results.
• Hot Coffee or Boiling Water: The hot liquid blooms the cocoa powder and makes the cupcakes more tender. Coffee enhances the chocolate flavor more than water, but if you don’t drink coffee, boiling water works.
• Vegetable Oil: Use a neutral oil like vegetable or canola. Don’t use olive oil, which will make the cupcakes taste weird.
• Cream Cheese: Must be fully softened to room temperature. See the tip box below for how to soften it quickly without making it greasy.
• Mini Chocolate Chips: Don’t use regular-sized chocolate chips. They’re too heavy and will sink in the cream cheese filling. Mini chips stay suspended throughout the filling so you get chocolate in every bite.

How to Soften Cream Cheese Quickly

Keep the cream cheese in its foil wrapper and submerge it in a bowl of warm water for 5-10 minutes. This softens it evenly without melting the outside, which keeps your filling smooth instead of greasy. If your cream cheese still has lumps after softening, beat it alone for 1-2 minutes until smooth before adding the egg and sugar.

Recipe FAQs

Can I use a different gluten-free flour blend?

I’ve only tested this recipe with Bob’s Red Mill 1-to-1 Gluten-Free Baking Flour (in the blue bag), which already contains xanthan gum, so I can’t guarantee results with other brands.

Why is my cream cheese filling lumpy?

Your cream cheese wasn’t soft enough. It needs to be completely soft (you should be able to easily press your finger into it). Beat the cream cheese alone for 1-2 minutes until smooth before adding anything else.

Can I use regular chocolate chips instead of mini?

I don’t recommend it. Regular chips are too heavy and will sink instead of staying suspended in the cream cheese. If you only have regular chips, chop them into smaller pieces.

Expert Tips

• Beat the cream cheese first. Beat the cream cheese alone for 1 minute before adding anything else. This breaks up any lumps and makes the filling silky smooth.
• Use a cookie scoop for even cupcakes. A cookie scoop makes it easy to portion the chocolate batter evenly into all 24 cups. Then use a tablespoon measure (or a #60 scoop) for the cream cheese filling.

Storage Instructions

Refrigerator: Store in an airtight container in the refrigerator for up to 5 days. Let them sit at room temperature for 20-30 minutes before eating.

Freezer: Flash freeze on a baking sheet for 1-2 hours, then wrap individually in plastic wrap and store in a freezer-safe bag for up to 3 months. Thaw at room temperature for 2-3 hours. Don’t microwave them or they’ll get gummy.

Serving Suggestions

Serve these with gluten-free lemon bars at your next party. The rich chocolate and cheesecake pairs well with tart lemon, and both can be made a day ahead and stack easily for transport without getting messy.

Add gluten-free raspberry crumb bars to create a dessert spread with variety. The fruity bars balance the chocolate cupcakes, and all three options travel well since none have delicate frosting. This gives guests a choice between chocolate, fruit, or citrus flavors.

Method

Make the Cheesecake Filling:

1. 1

   Preheat oven to 350°F. Line two 12-cup muffin pans with paper lines (you'll need 24 total). Set aside.

2. 2

   In a medium bowl, beat 8 oz cream cheese with a hand mixer or whisk for 1 minute until smooth and fluffy with no lumps.

3. 3

   Add ¼ cup granulated sugar, 1 large egg, and 1 teaspoon vanilla extract. Beat for 1-2 minutes until completely smooth and combined.

4. 4

   Stir in 0.75 cup mini chocolate chips, reserving the remaining ¼ cup for topping. Set the bowl aside.

Make the Chocolate Cupcake Batter:

1. 5

   In a large bowl, whisk together 3 cups gluten-free flour blend, 2 cups brown sugar, ⅔ cup unsweetened cocoa powder, 2 teaspoons espresso powder, 2 teaspoons baking soda, and 1 teaspoon salt until well combined with no lumps.

2. 6

   In a separate bowl or large measuring cup, stir together 2 cups hot brewed coffee (or boiling water), ⅔ cup vegetable oil, 2 tablespoons apple cider vinegar, and 2 teaspoons vanilla extract.

3. 7

   Pour the wet ingredients into the dry ingredients and stir until combined and smooth. The batter will be very thin and pourable.

4. 8

   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)

5. 9

   Spoon 1 tablespoon of the cheesecake filling onto the center of the chocolate batter in each cup. It will sink slightly, which is normal.

6. 10

   Sprinkle the remaining 0.25 cup mini chocolate chips evenly over all 24 cupcakes.

7. 11

   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.

8. 12

   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.