Why You’ll Love These Gluten-Free Cupcakes
There’s something magical about cutting into a black bottom cupcake and finding that creamy, tangy center tucked inside a deeply chocolatey base.
The chocolate batter bakes up dark and fudgy from a touch of espresso powder, while the cream cheese filling stays rich and just barely set.
- No frosting needed. The cream cheese filling bakes right into the center and comes out rich and tangy every time. Who needs frosting when the filling is this good?!
- Minimal cleanup. The batter comes together in one bowl and the filling in another. You’ll barely have any dishes to deal with!
- Make-ahead friendly. Bake these the night before and they’re just as good the next day. That makes them a great pick for parties or holiday baking.
What You Need
Here are a few notes on some of the key ingredients to make these gluten-free black bottom cupcakes. Jump to the recipe card below for the exact measurements.
- Cream cheese. Use it cold (straight from the fridge!) so the filling stays thick and dense enough to sink into the batter instead of spreading over the top.
- Vinegar. This batter skips eggs entirely, which is actually by design. The vinegar reacts with the baking soda to leaven the chocolate base and keep it light. It’s the classic trick from Depression-era wacky cake, and it makes these naturally egg-free and vegan (minus the cream cheese filling!).
- Unsweetened cocoa powder. Use natural, not Dutch-processed. Natural cocoa is acidic and reacts with the baking soda to leaven the cupcakes properly. Dutch-process has been neutralized, so the baking soda won’t activate the same way. I use the same kind in these gluten-free red velvet cupcakes!
- Mini chocolate chips. I switched to mini chips after testing with regular-size ones. The smaller chips stay suspended throughout the cream cheese filling so you get chocolate in every single bite.
How to Make Gluten-Free Black Bottom Cupcakes
Here’s an overview of how to make this recipe. You can jump to the recipe for the full instructions!
Make the filling. First, beat the cream cheese and sugar until smooth, then beat in the eggs and salt until well-combined. I use a rubber spatula to fold in the chocolate chips, then set the filling aside for now.
Make the batter. I whisk the dry ingredients together by hand in the bowl from my stand mixer. I like to let it do the work when I add the liquids, and this way I only use one bowl!
Erin’s Tip
On my second attempt making these cupcakes I added espresso powder. It really enhances the chocolate flavor! I also use it to deepen the chocolate in these gluten-free Hostess cupcakes.
Add the liquids. Mix in the liquid ingredients on medium speed until the batter is smooth. I find I always need to scrape the sides and bottom about halfway through get everything evenly mixed.
Prepare to bake. I use a kitchen scoop or large spoon to add the batter to the lined muffin pan. It’s important to only fill them halfway! Then add a dollop of filling to the center of each.
Erin’s Tip
You may have a little leftover cream cheese filling, and it’s too good to toss. Swirl it into brownie batter or drop spoonfuls onto pancakes while they cook for a creamy, cheesecake-y center.
Bake and cool. Bake the cupcakes for about 16-18 minutes. The cream cheese should still look pale. I recommend pulling them the moment the filling starts to take on any color. Cool them in the pan for 5 minutes, then let them cool the rest of the way on a wire rack.
Erin’s Tip
I always test my toothpick in the chocolate base, not the cream cheese center. A few moist crumbs means they’re done and the residual heat takes care of the rest.
More Gluten-Free Chocolate Recipes
Gluten-Free Black Bottom Cupcakes
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
- 1⅓ cups (200g) gluten-free measure-for-measure flour
- 1 cup (200g) granulated sugar
- 1 teaspoon baking soda
- ⅓ cup (27g) unsweetened cocoa powder (not Dutch-processed)
- ¼ teaspoon instant espresso powder, optional
- ½ teaspoon kosher salt
- ⅓ cup (80ml) neutral oil
- 1 tablespoon white distilled vinegar
- 1 teaspoon vanilla extract
- 1 cup (240ml) hot water
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.
