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!

Table of Contents

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

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!
They’re almost a muffin, so you can eat them for breakfast.
They’re great for parties as they won’t get messed up in transit since there’s no frosting.
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.

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!