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.
Jaime says
i have seen these popping up everywhere and now i want to make them! they look perfect, thanks for listing your modifications for us
Aimée says
Ok, so this is new to me! Hope that encourages you. I have a lot of similar feelings about blogging- it’s been a great journey.
I’ll be making these soon! They look great.
hot garlic says
You have to know I feel you on that one! It is hard to strike a balance once people start to read it and follow you isn’t it!? You feel like you then have to please them!
I think this is great, though I have heard of them a hundred times, it never gets old and I still haven’t made them. Maybe this will be the time!
Jacque says
Well, I haven’t seen anyone blog about these that I can remember, so I’m glad you did. They look fantastic….mmmm, really! I like how the cheesecake stays in the middle, just like it should. 🙂
Elle says
Another great recipe from that great book! Love that the cheesecake stays in the middle…and the glaze is just the thing to top ’em with. It really is awesome when someone finds a post from the past and comments that it is what they were looking for…and they made it, too! Bet someone will do that with these great cupcakes!
kamailesfood says
Mmm…these look great. Even when something’s been done a bazillion times, I enjoy seeing other people’s versions.
eatme_delicious says
I agree – you have this blog because you love food and posting/writing about the stuff you make, so who cares if other people have made the same thing. I’ve seen these done many times but never with a chocolate glaze which seems like the perfect addition!
Rosie says
Hi Deb, I have an award waiting on my blog for you 🙂
http://rosiebakesapeaceofcake.blogspot.com/
Rosie x
Debbie says
The cupcakes look great. I would love to try them. It is hard to come up with new things to make a blog interesting. Sometimes I think mine is kind of boring, but it is so much fun and you just can’t come up all the time with something new. I post things that probably have been made a million times, but it is STILL fun!!!!!
Kate / Kajal says
i hear ya girl …i feel that way about my food n photographs too .. !
and its always nice to see a chocolate recipe …even if its done a 100 times over !! 🙂
love the picture where of the cross section … shows what you’re gonna get !
Prudy says
This one’s definitely worth doing again. I haven’t made these in ages and I don’t want to forget about them. They’re so good and pretty easy and everyone always loves them.
Paula says
I hope you keep on blogging! I love looking at your creations and enjoy the narratives that accompany them! These cupcakes are no exception! How do you keep from, you know, eating them without stopping? I love your colorful cupcake cups, too. I wonder if these would hold up in a lunch box. My family would go nuts over these! YUM!
giz says
I’m so intrigued by black bottom cupcakes. I have to tag this one and try it. They’ll be putting a sign on my door soon that says “muffins r us”…
They look so good.
Psychgrad says
Maybe I should consider redundancy of recipes, but I really never do. I just like to post fruits of my labour, successful or not. I think we’re all learning from each other.
Plus, the more I see a recipe, the more I want to make it myself. So, repetition is good.
I have seen black bottom cupcakes before. But now I’m reminded that I really should make them.
Mrs. L says
And just because they’ve been done a hundred times before, doesn’t mean that every has done them! I’ve never made these nor do I have a recipe for them bookmarked so know that they will now go on my list of things to make.