These Black Bottom Cupcakes are a classic dessert that combines a rich chocolate cupcake and a creamy chocolate chip cheesecake filling. They’re moist, tender and rich with the perfect blend of texture and flavor. Not to mention easy to make!

Black bottom cupcakes stacked on a wire rack

Black bottom cupcakes offer the best of both worlds with a moist chocolate cupcake and creamy chocolate chip cheesecake filling. They’re a classic, old-fashioned recipe that is kind of like a cheesecake cake in cupcake form (think Hershey’s chocolate bar cheesecake cake with fewer layers). I’m not sure exactly where or how they originated, but it seems to be in Maryland, as they’re sometimes referred to as Baltimore black bottom cupcakes and can be found in every store and bakery in the region.

What Makes These Cupcakes Different

My black bottom cupcakes recipe deviates from the classic a bit. Here’s how:

Vinegar – There’s no vinegar in the cupcake batter. Contrary to what you might read, it’s not necessary to react with the baking soda to rise – cocoa powder is acidic and does that.
Cocoa powder – I added a little extra cocoa to ramp up the chocolate flavor a bit.
Eggs – I also used an egg. Many recipes don’t use one, but I think it really improves the texture of the cupcakes and helps keep them from drying out in the fridge.

Why These Black Bottom Cupcakes Are So Good

Two desserts in one. These cupcakes combine two desserts – moist chocolate cupcakes and tangy cheesecake into one dessert. I love the combination of the creamy cheesecake and soft cupcake in every bite.
The cheesecake filling. I add mini chocolate chips to my filling so there’s extra dots of chocolate in every bite. It’s smooth and creamy and just the right balance of tangy and sweet.
Moist chocolate cupcake. The rich chocolate cupcake makes up the “black bottom” of this dessert. The crumb is moist and tender but sturdy enough to hold the weight of the cheesecake filling.

Ingredient Notes

Here’s a look at the ingredients needed to make these cupcakes and a few important tips. The exact measurements can be found in the recipe card below.

Overhead view of ingredients necessary to make black bottom cupcakes

Cream cheese – Be sure to use full fat, brick-style cream cheese. Reduced fat or tub cream cheese can be too thin.
Egg – Helps bind the cheesecake ingredients together. I like to use an egg in the cupcakes as well, though some recipes don’t, because I find it keeps them moist longer when stored in the fridge and adds a better texture overall.
Salt – Enhances the flavors already present.
Mini chocolate chips – I recommend mini chocolate chips because they distribute more evenly in the filling.
All-purpose flour – Use a food scale or the spoon and level technique, as described in my post on How To Properly Measure Flour, to ensure accurate measuring. Too much or too little will affect the final texture of the cupcakes.
Milk – Whole milk or 2% work best.
Vegetable oil – Adds more lasting moisture to these cupcakes and helps them stay tender, even when cold from the fridge.

A black bottom cupcake with the wrapper pulled down and a bite missing to show the inside

How To Make Black Bottom Cupcakes

These cheesecake-filled cupcakes are super easy to make. The two individual parts come together quickly. The printable instructions can be found in the recipe card below.

Begin by adding cupcake liners to the cupcake pan and preheating the oven to 350°F.

Whisking cream cheese filling ingredients together

Beat the cream cheese and sugar until smooth. Mix in the egg, salt, and vanilla extract.

Folding mini chocolate chips into cream cheese filling

Stir in the mini chocolate chips. Set aside.

Whisking dry cupcake ingredients together

Combine the dry ingredients in a bowl.

Whisking egg into dry cupcake ingredients

Add the milk, oil, egg, and vanilla extract.

Chocolate cupcake batter in a bowl with a whisk

Whisk until well combined and smooth.

Chocolate cupcake batter and cheesecake filling in cupcake liners

Fill each liner 1/3 full with batter. Add 1 1/2 tablespoons of cheesecake on top.

Bake for 16-19 minutes. Cool in the pan for 3-5 minutes then transfer to a cooling rack.

Tips for the Best Cupcakes

Here are a few of my best tips for making perfect black bottom cupcakes every time.

Don’t soften the cream cheese too much. While the cream cheese should be at room temperature, you do want to make sure it’s not too soft. If it is, the cheesecake mixture won’t hold together as well on top of the cupcake and will spread out over the top.
Prevent the cheesecake from sinking. Be sure not to drop a big ball of the cheesecake mixture in the middle of the cupcake, or it’ll mostly sink to the bottom and you won’t see it much. You want the cheesecake to spread a bit on top of the batter.
Don’t add too much cupcake batter. It’ll engulf the cheesecake as it rises and cover it entirely.
Check for doneness. I recommend checking these at the 16-minute mark to ensure they don’t overbake. They’re ready when a toothpick inserted in the cupcake comes out clean and the cheesecake looks set.

Overhead view of Black bottom cupcakes on a wire rack

Proper Storage

Fridge: Black bottom cupcakes need to be stored in the fridge due to the cream cheese filling. Keep in an airtight container and enjoy within 4-5 days.
Freezer: Once they’ve cooled completely, they can be wrapped in plastic wrap and placed in an airtight container. Freeze for up to 3 months.