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.
Chocolate black bottom cupcakes with cream cheese centers topped with chocolate chips in a muffin tin.
Want to save this recipe?
Just enter your email and get it sent to your inbox! Plus you’ll get new recipes from us every week!

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.

Ingredients for a recipe arranged on a marble surface, including gluten-free flour, cocoa powder, sugar, water, neutral oil, an egg, cream cheese, chocolate chips, vinegar, vanilla, espresso powder, baking soda, and salt.
  • 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!

A hand pours a metal measuring cup of chocolate chips into a mixing bowl containing a light-colored batter.

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.

A metal mixing bowl containing dry ingredients including flour and cocoa powder being whisked, surrounded by measuring cups and eggshells.

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.

A metal mixing bowl containing smooth chocolate batter, surrounded by a whisk, eggshells, and small bowls of ingredients on a marble countertop.

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.

A muffin tin filled with twelve chocolate cupcakes, each topped with a dollop of cream cheese filling.

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.

Twelve chocolate black bottom cupcakes with dollops of cream cheese and chocolate chips in a baking pan.

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.

A chocolate black bottom cupcake with a white cream cheese center and chocolate chips, with a large bite taken out of it.

More Gluten-Free Chocolate Recipes

Several chocolate cupcakes with cheesecake centers and chocolate chips, one with a bite taken out of it.
No ratings yet

Gluten-Free Black Bottom Cupcakes

Author Erin Collins
Prep Time 20 minutes
Cook Time 18 minutes
Total Time 38 minutes
Servings 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!
Pin It Comments Print

Video

Save this recipe!
Just enter your email and get it sent to your inbox! Plus you’ll get new recipes from us every week!

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

This post may contain affiliate links. Please read our disclosure policy.

Categories: , ,

Hi, I'm Erin!

BS Food Science,

MS Nutrition

I believe you can make amazing, gluten-free food with everyday ingredients that everyone will enjoy. I'm here to share my tried-and-true recipes with you!

Read about Erin

You may also like

Comments

    1. Hi Sharon! Yes we’ve used Violife with this recipe and it works well. We hope you love the cupcakes!

      Reply

  2. Is there any other topping you can use instead of the cheesecake filling? Just wondering about others flavors that will work well with the chocolate?

    Reply

  3. I’m confused abt the egg listed in the ingredient pic and the directions. But it also says that this recipe is entirely egg free because of the vinegar and baking soda. Can anyone help me figure this out? Need to bake them tomorrow…

    Reply

    1. Hi Lisa! The egg is used in the cream cheese filling. The cupcake batter is completely egg-free and vegan using vinegar and baking soda instead, but the cream cheese filling is not egg-free or vegan. We hope this helps clarify! Thank you for your question!

      Reply

    1. Hi Megan! Replacing the hot water and espresso powder with hot coffee should work well. We hope you love the cupcakes!

      Reply

    1. Hi Catey! Avocado oil and vegetable oil are two of our typical go-to neutral oils. We hope you love the cupcakes!

      Reply

Leave a Reply

Your email address will not be published. Required fields are marked *

Recipe Rating