A childhood favorite that we called chocolate cheesecake cupcakes, these Black Bottom Cupcakes are a classic! A dark chocolate cupcake is topped with a cheesecake mixture in these easy cupcakes that are simply irresistible!
For another twist on the cheesecake, try these Mini Cheesecakes.

Black Bottom Cupcakes – or Chocolate Cheesecake Cupcakes are what we called them – are a nostalgic childhood treat for me. I remember my mom making them often.
I originally posted a version of these Black Bottom Cupcakes back in 2008. I posted a version that had a chocolate ganache, but I had to go back to this classic version, because they are just so good that you don’t need any kind of topping or frosting on them. And while I’m pretty sure my mom’s cupcakes stared with a cake mix, these are made from scratch, but I promise they aren’t much harder than a box mix.
Ingredients
- Cream Cheese: Use full fat cream cheese for the best results.
- Sugar: I use granulated sugar for the filling.
- Egg: The egg is important because it provides the structure for the cheesecake filling.
- Salt: Salt will help to balance the flavors.
- Vanilla: You’ll need vanilla extract for both the cheesecake filling and the cupcakes.
- Chocolate Chips: You can use full sized chocolate chips or mini chocolate chips, but I much prefer mini chocolate chips for these cupcakes.
- Flour: I use unbleached all-purpose flour.
- Sugar: The original recipe I had posted here had both granulate and brown sugar, and after testing, I found that there wasn’t a big flavor or texture difference. So I use just granulated sugar to keep things easy.
- Cocoa Powder: I use a regular unsweetened cocoa powder, like Hershey’s or Nestle.
- Baking Soda: The baking soda gives the cupcakes their rise. It’s especially important in this recipe because there are not any eggs in the cupcakes.
- Water: You will need boiling water for the cupcakes. The boiling water will help the cocoa powder to “bloom”, bringing out a deeper chocolate flavor.
- Oil: You can use any neutral flavored baking oil. Some examples are vegetable oil, canola oil, or avocado oil.
- Vinegar: The vinegar will react with the baking soda to create the rise for the cupcakes. I use apple cider vinegar, but regular white vinegar will work, as well.
How to Make Black Bottom Cupcakes
STEP 1: Start by making your cheesecake filling. Beat the cream cheese until it is smooth. Then beat in the sugar, followed by the egg and vanilla.
STEP 2: Stir your chocolate chips into the mixture, making sure to scrape the sides and the bottom of the bowl to make sure everything is incorporated. Set this aside.
STEP 3: Make the cupcake batter by mixing together the flour, sugar, cocoa powder, baking soda and salt. It’s best to whisk this together to make sure everything is fully combined.
STEP 4: In another bowl, or I like to use a liquid measuring cup to save on dishes, combine the boiling water with the oil, vinegar, and vanilla. Add this to the dry ingredients and mix until the batter is thick and smooth.
STEP 5: Add the batter to prepared muffin tins, filling each about 1/2 full of batter. Don’t overfill these!
STEP 6: Divide the cheesecake mixture evenly to the tops of the cake batter. I used a 1 1/2 tablespoon scoop for the filling, and added a slightly heaping scoop to each cupcake. Bake until cooked through, then let cool completely before serving.
Tips and Tricks
- My favorite way to eat these cupcakes is the next morning, straight from the refrigerator. I think they are pure magic when they are cold!
- I purposefully like these to sink down some in the center. Maybe it’s because it reminds me of the cupcakes of my childhood. But I went through several test rounds of these cupcakes, and had to get them so that the cheesecake mixture sinks into the middle a bit and doesn’t just sit on top. So don’t think you’ve done something wrong!
- I found that making 20 cupcakes was just about perfect. I tried to keep it to 12, 18, or 24, but the ratios were never perfect for me. But 20 gave me the perfect ratio of cupcake to cheesecake filling.
More Favorite Chocolate Cupcake Recipes
Devil’s Food Cupcakes with Fluffy Frosting
Ultimate Chocolate Cupcakes
Chocolate Cupcakes with Raspberry Filling
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Black Bottom Cupcakes
Ingredients
Filling:
- 8 ounces cream cheese softened
- 1/3 cup granulated sugar
- 1 large egg
- 1/4 teaspoon salt
- 2 teaspoons pure vanilla extract
- 3/4 cup mini chocolate chips
Cupcakes:
- 1 1/2 cups all purpose flour
- 1 cup granulated sugar
- 1/2 cup unsweetened cocoa powder
- 1 teaspoon baking soda
- 1/2 teaspoon salt
- 1 cup boiling water
- 1/2 cup neutral cooking oil (vegetable, canola, avocado, etc)
- 1 tablespoon apple cider vinegar
- 2 teaspoons pure vanilla extract
Instructions
- Preheat the oven to 350ºF. Line 20 muffin cups with liners.
- In a bowl, beat the cream cheese until smooth. Add the sugar and beat in fully. Add the egg, salt and vanilla and continue to beat until combined. Stir in the chocolate chips. Set aside.8 ounces cream cheese, 1/3 cup granulated sugar, 1 large egg, 1/4 teaspoon salt, 2 teaspoons pure vanilla extract, 3/4 cup mini chocolate chips
- In another bowl, whisk together the flour, granulated sugar, cocoa powder, baking soda, and salt.1 1/2 cups all purpose flour, 1 cup granulated sugar, 1/2 cup unsweetened cocoa powder, 1 teaspoon baking soda, 1/2 teaspoon salt
- In a large liquid measuring cup, or in another bowl, mix together the boiling water, oil, vinegar, and vanilla. Pour the liquid into the dry ingredients and mix jus until combined.1 cup boiling water, 1/2 cup neutral cooking oil, 1 tablespoon apple cider vinegar, 2 teaspoons pure vanilla extract
- Fill each liner about 1/2 full of the the batter.
- Top each with some of the cheesecake filling. (Each should take just over 1 1/2 tablespoons of batter.)
- Bake in the preheated oven for 18-20 minutes, or until cooked through.
- Let cool completely, then store in the refrigerator.
michelle @ TNS says
you can’t go wrong with a classic!
Gigi says
the cupcakes look sinfully delicious! and i love the book. i bought after i did the cheesecake pops and have used it a lot since!
HoneyB says
Oh this looks delicious!
noble pig says
I love a cupcake with a surprise inside, thank you!
Mary says
I’m going to bookmark this recipe for my favorite young visitors..
Suzana says
Fabulous cupcakes! Love the flavour combination – just bookmarked the recipe. 🙂
Brilynn says
I never mind seeing the same recipe two or three, (or four…) times because it just reassures me that it really is a good recipe that is worth trying out. Food bloggers have yet to let me down.
mimi says
i have been eyeing making these kind of cupcakes for like forever now! yours came out looking amazing!
Cakebrain says
There’s a reason why these are done again and again, I suppose…they look so fantastic!
Heather says
oh my gosh, those look amazing! i almost licked my screen!
Ruth says
Oh my goodness! These look fabulous! I am tagging these on my reader so my girls can bake these in the next couple weeks. Thank you!
Maria says
I have actually never made these! Shocking I know!! They do look divine, so I must try them soon!! I am always in the mood for a good sweet treat!
The Mediocre Cook says
These do look absolutely amazing and your right. Sweets like these can never be posted enough about.
Lizzybee says
I can’t wait to try these!
Erin says
These look delicious! I’ve made black bottom brownies and they were delicious, but I haven’t made cupcakes yet. I love the chocolate and cream cheese combination.
Happy cook says
Wow looks so delicious.
It is coffee time now here and i would love to have atleas 2 of them with my cuppa