These black bottom cupcakes are a classic cupcake recipe that’s moist, rich, but airy. The cupcakes consist of two parts: a fudge-like base and a luscious cheesecake filling dotted with chocolate chips. It’s like having the best of both worlds when you cannot decide on making a cake or cheesecake, all in a bite-sized cupcake form!

These cupcakes are so simple to make but are such a decadent treat that’s full of flavor. I love making them for parties, and they always disappear fast at bake sales. If you want another crowd-pleasing cupcake recipe, try my chocolate cupcake recipe, lemon cupcake recipe, and red velvet cupcake recipe.

What You Need to Make This Recipe

Cream cheese — be sure to use full-fat cream cheese and not the spreadable type from a tub. Cold cream cheese won’t mix well, so bring it to room temperature, or it’ll leave small lumps in the filling.

Chocolate chips — you can use regular chocolate chips or mini chocolate chips. I prefer mini chocolate chips so each bite is filled with chocolate chips. You can also use any chips in this recipe, such as dark chocolate, white, milk chocolate, or semi-sweet.

Cocoa powder — I use unsweetened cocoa powder for this recipe and not Dutch-process cocoa powder. Dutch-process cocoa powder has been neutralized in an alkaline solution which means it won’t react with the baking soda to give the cupcakes a good rise.

Vinegar — when you combine white vinegar and baking soda in the batter, it releases carbon dioxide and causes the cupcake batter to rise, making for a moist, fluffy texture. If you skip the vinegar, you may end up with a dense cupcake.

How to Make Black Bottom Cupcakes

1. In a medium bowl, beat the cream cheese and sugar with a mixer on medium speed until smooth.

2. Add the egg and salt. Beat until well combined.

3. Stir in chocolate chips.

4. Whisk together the flour, sugar, cocoa, baking soda, and salt in a large bowl.

5. Whisk together the water, oil, vinegar, and vanilla in a small bowl.

6. Add the water mixture to the flour mixture, stirring until well combined and smooth.

7. Divide the chocolate batter evenly among the paper liners in a muffin pan.

8. Spoon the cream cheese mixture into the center of the chocolate batter in each liner. Bake for 16 to 18 minutes or until a wooden pick inserted into the chocolate cake comes out clean, and the cream cheese filling is set. Let the black bottom cupcakes cool in the pan for 5 minutes before removing them from the pan and cool completely on a wire rack.

Pro Tips for Making This Recipe

Measure your flour correctly! Adding too much flour to the recipe is the most common mistake that will yield dry and dense cupcakes. The best and easiest way to measure flour is by using a scale. If you don’t have one, then fluff your flour with a spoon, sprinkle it into your measuring cup, and use a knife to level it off.
The egg should be at room temperature to ensure it incorporates into your batter evenly. If you forgot to take your egg out of the fridge ahead of time, you could quickly bring it to room temperature by placing it in a large bowl and running warm tap water over it for 5 minutes.
Avoid overmixing as you risk over-developing the gluten in the batter leading to this black bottom cupcake recipe becoming tough.
Don’t skip sifting the dry ingredients. Doing so will remove any clumps and aerates the ingredients to yield lighter cupcakes.
Use paper liners as the cupcakes will stick to the muffin pan if you add the batter directly to the pan.
Try my tasty chocolate buttercream frosting recipe or vanilla buttercream frosting if you want to have frosted cupcakes.

Frequently Asked Questions

Do these cupcakes have to be refrigerated?

Due to the cream cheese, you will have to refrigerate the cupcakes. Before serving, you can bring them out to room temperature or serve them directly from the fridge.

Can I make these in advance?

Yes, you can bake the cupcakes in advance. Refrigerate them in an airtight container for up to 5 days. You cannot make the batter in advance as the cupcakes will fall flat, as the activated baking soda will lose its rising properties.

Can I freeze these?

I like to freeze the black bottom cupcakes on a baking sheet, then transfer them to a freezer-safe bag. Store for up to 2 months. When ready to eat, thaw in the fridge overnight before serving.

If you love this recipe try these out!

If you’ve tried this Black Bottom Cupcakes recipe, then don’t forget to rate the recipe and let me know how you got on in the comments below, I love hearing from you!

Black Bottom Cupcakes