These Black Bottom Cupcakes are marbled works of art that practically melt when you bite in! They are rich, chocolatey, and super moist, with the creamiest chocolate chip cream cheese filling you'll ever taste!

Cream cheese filled chocolate cupcakes topped with semi-sweet chocolate chips randomly placed on a light gray background.

Why You’ll Love This Recipe

These cream cheese-filled black bottom chocolate cupcakes were a favorite treat when I was a kid, and they still are as an adult!

This easy-to-make classic makes over two dozen moist, rich chocolate cupcakes with a luscious cream cheese filling topped with semisweet chocolate chips. It's both a cake and a cheesecake in one, and the best part is no frosting is needed!

They’re perfect for birthday parties, family gatherings, book clubs, and holidays. Trust me, they're so good that they'll vanish the moment you put them out! If you're hosting a smaller get-together, cut the recipe in half or try my Small Batch Black Bottom Cupcakes, which make only six!

For more crowd-pleasers, give my Devil’s Food Cupcakes, Red Velvet Cupcakes, or Mint Chocolate Cupcakes a try!

What You'll Need

These are the ingredients I suggest for making these easy black bottom cupcakes. The items in the bulleted list are the key ones that need a little more explanation.

Ingredients in various size bowls labeled as water, semisweet chocolate chips, apple cider vinegar, all purpose flour, granulated sugar, cream cheese, baking soda, vegetable oil, vanilla extract, eggs, and unsweetened cocoa powder on a white marbled background.

Apple Cider Vinegar. White vinegar can stand in for it. The vinegar reacts with the baking soda, and that pair releases carbon dioxide, which lifts the batter into light, fluffy cupcakes. Don’t leave this one out.
Baking Soda. Check that yours is still active before you start. Stir a spoonful of baking soda into a little vinegar or lemon juice. If it fizzes, it's fresh. If it barely reacts, buy a new box.
Cream Cheese. Pick full-fat cream cheese in a block, not the tub-style kind. The original Philadelphia brand has always been my go-to. Let it soften to room temperature before you begin.
Semi-Sweet Chocolate Chips. Milk chocolate, dark chocolate, regular, or mini chips all work here. I like Ghirardelli best, but honestly, any brand will do the job.
Unsweetened Cocoa Powder. I used Hershey’s unsweetened cocoa powder, but choose whichever brand you like. Do not swap in Dutch process cocoa, because it won't react with the baking soda.

Cream cheese filled chocolate cupcakes topped with semi-sweet chocolate chips randomly placed on a light gray background with center cupcake unwrapped and sliced in half to see the cream cheese center.

How to Make the Recipe

Here's a quick overview of how to make these black bottom cupcakes. For the complete printable recipe, which you can view in US customary or metric measurements with the toggle switch, see the recipe card below.

Chocolate Chip Cream Cheese Filling

Softened and beaten cream cheese in a glass mixing bowl on a white marbled background.

Step 1. Beat the cream cheese until smooth. Add the sugar and egg.

Chocolate chips folded into cream cheese filling in a glass mixing bowl on a white marbled background.

Step 2. Fold in the chocolate chips with a spatula. If you like, chill the mixture until you're ready to add it to the batter.

Chocolate Cupcakes

Whisked dry ingredients for black bottom cupcakes in a glass mixing bowl on a white marbled background.

Step 1. Whisk the dry ingredients. Combine the flour, baking soda, unsweetened cocoa powder, and sugar.

Black bottom cupcake batter mixed fully together in a large glass mixing bowl on a white marbled background.

Step 2. Mix in the wet ingredients. Add the eggs, vegetable oil, water, vinegar, and vanilla extract, and mix just until combined. The batter will be fairly thin.

Metal cupcake tin with cupcake liners filled with chocolate cupcake batter placed on a white marbled background.

Step 3. Fill the liners. Use a cookie scoop to fill each liner no more than 1/2 full.

Metal cupcake tin filled with chocolate cupcake batter topped with chocolate chip cream cheese filling on a white marbled background.

Step 4. Add 1-2 tablespoons of the cream cheese filling on top. If you want, press in a few extra chocolate chips.

Baked black bottom cupcakes in a metal cupcake tin on a white marbled background.

Step 5. Bake the black bottom cupcakes for 22-24 minutes at 350ºF. Every oven is different, so start checking at the earliest suggested time.

Cooling chocolate chip cream cheese filled chocolate cupcakes on a wire cooling rack on a white marbled background.

Step 6. Take them out and cool. Let the cupcakes rest in the tin for about 10 minutes, then move them to a wire rack to cool completely.

Fixing Lumpy Cream Cheese

If you end up with the dreaded lumpy cream cheese while making these black bottom cupcakes, try these handy fixes.

Microwave it. Put the cream cheese mixture in a microwave-safe bowl and heat it in 10-15 second bursts to soften it. Don't heat it too long, or you'll cook the egg. Whisk again until the lumps are gone.
Try a food processor. Transfer the cream cheese mixture to a food processor and pulse for a few seconds.
Start over. Warming it has worked for me before, but sometimes nothing fixes it. In that case, begin again with room-temperature cream cheese and a room-temperature egg.

Cream cheese filled chocolate cupcakes topped with semi-sweet chocolate chips placed tightly together on a light gray background.

Helpful Tips

Let your eggs come to room temperature before you start so they blend smoothly into the batter.
Soften the cream cheese to room temperature. Even slightly cold cream cheese can leave small lumps in the filling and make it look like cottage cheese.
Don't overmix the cupcake batter, since that overdevelops the gluten and leads to dense, tough cupcakes.
Fill the liners only halfway so there's room for a dollop of cream cheese filling.
I strongly suggest using an oven thermometer to confirm your oven is calibrated to the right temperature.
This easy black bottom cupcake recipe also works in a 13″ x 9″ x 1″ baking pan. Bake at 350°F for 40-45 minutes.
This recipe yields about 30 cupcakes. If that's more than you need, cut the recipe in half.

Common Questions

How many cupcakes does this black bottom cupcakes recipe yield?

This recipe makes about 30 cupcakes. You can halve the recipe or try my Small Batch Black Bottom Cupcakes instead!

Can this black bottom cupcakes recipe be made as a cake?

Yes! You can bake this as a sheet cake in a 13″ x 9″ x 1″ baking pan. Bake at 350°F for 40-45 minutes.

Is apple cider vinegar the same thing as apple cider?

No, and they should not be swapped for one another. Apple cider is a fall drink. Apple cider vinegar is a baking acid that reacts with the baking soda to give the cupcakes an airy texture.

What can I use in place of apple cider vinegar?

You can use distilled white vinegar instead.

If you make this Black Bottom Cupcakes Recipe or anything else from my website, please give it a star rating and tell me how it turned out in the comments below. Thanks for stopping by!