Gluten-Free Black Bottom Cupcakes

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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!
A photo of a gluten-free black bottom cupcake with cheesecake filling and topped with mini chocolate chips on a marble table.
A classic dessert gets a makeover with these gluten-free black bottom cupcakes. Rich chocolate cupcakes are filled with a chocolate chip cheesecake center for a decadent and tasty gluten-free dessert.
A photo of a gluten-free black bottom cupcake with cheesecake filling and topped with mini chocolate chips on a marble table.
It’s no secret that I like to make baked goods for my friends, family, and coworkers. One of the biggest struggles I have is how to successfully transport those yummy gluten-free baked goods from point A to B without messing them up.

That’s where these gluten-free black bottom cupcakes come in. They have no frosting, so there’s nothing to mess up! You can stack them for easy transport and they remain as perfect (and delicious) as can be!
Black bottom cupcakes work beautifully as a dessert and can even pass a chocolatey breakfast treat! If you’re looking for an easy and tasty gluten-free dessert recipe, this is it! Trust me, your families/friends/coworkers will thank you!

What are black bottom cupcakes?

Black bottom cupcakes are essentially a chocolate cheesecake cupcake. A moist, gluten-free chocolate cupcake is topped with a rich chocolate chip cheesecake filling. In fact, they have no frosting at all!
Black bottom cupcakes get their name from having the chocolate cake fall to the bottom of the cupcake and the cheesecake filling sits on top. Since the cheesecake is heavier than the chocolate cupcake batter, it does fall into the center a bit.
The black bottom cupcake originated sometime in the 1900’s. I haven’t found a clear indication of where this recipe idea started, but one thing everyone can agree on is they remember their grandmas making them!
A photo of a muffin tin filled with gluten-free chocolate cheesecake cupcakes

What makes these black bottom cupcakes gluten-free?

I use a gluten-free flour blend to make these chocolate cupcakes gluten-free. Bob’s Red Mill 1-to-1 Gluten Free Baking Flour is a favorite in this recipe, but I’ve also used Cup4Cup and my own flour blend with great results.
If your gluten-free flour blend does not already contain xanthan gum, you’ll want to add it.
Be aware that not all gluten-free flour blends are created equal and I can only vouch for the ones I’ve tested in this black bottom cupcake recipe.
If you do try any other gluten-free flour blends, please let me know the results so I can add them to the list!

Why you should make these chocolate cheesecake cupcakes

  1. They’re beyond easy to make. They do have two main parts that you have to make, just like normal cupcakes, but I love that all of the work is done up-front before baking and there’s no frosting necessary!
  2. They’re almost a muffin, so you can eat them for breakfast.
  3. They’re great for parties as they won’t get messed up in transit since there’s no frosting.
  4. They’re on the table in under 45 minutes.

How to Make Black Bottom Cupcakes

There are two parts to making these easy gluten-free chocolate cheesecake cupcakes, but I promise you it’s so simple! First, you need to make the chocolate cupcake batter and then you’ll make the cheesecake filling.
The chocolate cupcake batter is so easy as it’s oil based and contains no eggs in it. All you have to do is mix together the gluten-free flour blend, xanthan gum (if using), brown sugar, cocoa powder, espresso powder, baking soda, and salt together.
A photo showing the process of mixing together the batter for gluten-free chocolate cheesecake cupcakes.
Then, add in the wet ingredients: coffee (or boiling water),vegetable oil, apple cider vinegar and vanilla together. Mix and you’re done.
Portion out the chocolate batter into the muffin tin lined with cupcake liners.
Then, make the cream cheese filling by blending together softened cream cheese, sugar and egg. Then stir in mini chocolate chips!
Place a dollop of cream cheese filling on top of every chocolate cupcake and then bake in the oven!
A photo showing the process of mixing chocolate cupcake batter and topping with cream cheese filling for gluten free black bottom cupcakes.
These cupcakes taste best when cooled and are a dream to pack-up and travel with to parties.

Can I make this recipe dairy-free?

You bet! Since the chocolate cupcake recipe already does not contain any milk or butter, all you need to change is the cheesecake filling.
Use a dairy-free or vegan cream cheese for the cheesecake filling and use dairy-free chocolate chips.
That’s it!

How to Store Leftover Gluten-Free Black Bottom Cupcakes

These black bottom cupcakes will keep at room temperature in an airtight container for 2-3 days.

If you’d like to keep these for longer, I’d suggest freezing them. You can flash freeze them on a baking sheet and then wrap or store in an airtight container.

Let defrost at room temperature for a few hours before eating. I wouldn’t suggest microwaving these to defrost.

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

Tips and Tricks for Making Gluten-Free Black Bottom Cupcakes

  • I like to use coffee in my batter to bring out the chocolate flavor, but you can also use boiling water instead.
  • The espresso powder also highlights the chocolate flavor and is optional if you do not have it on hand.
  • Make sure your cream cheese is softened so that it is silky smooth and doesn’t have any clumps when mixed together with the egg.
  • I highly suggest using mini chocolate chips as opposed to regular-sized chocolate chips. It keeps the cheesecake light and fluffy and is the perfect chocolate to cheesecake ratio. You could also use roughly chopped up chocolate if you prefer.

Looking for more gluten-free cake, cupcake and muffin recipes? Try these!

Go crazy for these gluten-free chocolate recipes!

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

Gluten-Free Black Bottom Cupcakes Recipe

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

Ingredients

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

Instructions

  • 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.

Nutrition

Serving: 24cupcakes | Calories: 260kcal | Carbohydrates: 38g | Protein: 3g | Saturated Fat: 8g | Cholesterol: 18mg | Sodium: 234mg | Fiber: 2g | Sugar: 25g
Tried this Recipe? Tag me Today!Mention @ADashofMegnut or tag #adashofmegnut!

This recipe was originally posted on January 18, 2010 and was updated on July 12, 2019 with an updated recipe, photos and tips and tricks to help you make these gluten-free black bottom cupcakes perfectly every time!

A photo showing the process of baking gluten free black bottom cupcakes.

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