Best chocolate cheesecake cupcakes! These black bottom cupcakes have moist chocolate cake filled with chocolate chip cheesecake filling.

These chocolate cheesecake cupcake recipe makes one of my all-time favorite desserts! Every year for my birthday, I would either have these cupcakes or rice krispies treats instead of birthday cake.
They’re so good that this year my daughter carried on the tradition by requesting these for her birthday.
I’m not sure whether it’s the moist chocolate cake or the rich cheesecake filling that makes them so good, but the combination of the two is unbeatable!
And don’t feel like you need to save these for a special occasion. The cupcakes are so easy that they’re perfect for any time you need a treat!
How to make chocolate cheesecake cupcakes

Step 1: To make the filling, beat the cream cheese, sugar, egg, and salt together until well-combined.
Step 2: Stir in the mini chocolate chips. Set aside.

Step 3: Melt the 1/2 cup semisweet chocolate chips over hot, not boiling, water, stirring until smooth. Remove from heat and set aside.
Step 4: In a large bowl, stir sugar, oil, egg, and vanilla together until well-combined. Stir in melted chocolate chips.

Step 5: Add flour, baking soda, and salt. Stir in just until combined. The batter will be very thick.
Step 6: Mix in the warm water just until combined. Batter will be thin.

Step 7: Divide half of the cupcake batter between the muffin tin cups.
Step 8: Drop a rounded tablespoon of filling in each muffin tin cup.

Step 9: Top with the remaining half batter.
Step 10: Bake.
Step 11: Cool in pan for 5 minutes. Remove to wire cooling rack to finish cooling.

Tips
- Cream cheese: I’ve used full-fat and reduced-fat cream cheese in this recipe. However, I don’t recommend fat-free cream cheese.
- Mini chocolate chips: I like to use mini chocolate chips in the filling because they don’t sink the way that regular-sized chocolate chips can. You can use regular-sized chocolate chips if you prefer.
- Water: The water should be about 80F. Cold water is more difficult to mix in, and the water should not be boiling water.

How to store
I store the cupcakes in a resealable container at room temperature for up to 4 days. You can also store the cupcakes in the fridge, if you prefer.
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Chocolate Cheesecake Cupcakes
Equipment
- Muffin tin
Ingredients
Cheesecake Filling
- 6 ounces cream cheese softened
- 1/4 cup granulated sugar
- 1 large egg
- Pinch salt
- 1/2 cup mini semisweet chocolate chips
Cupcakes
- 1/2 cup semisweet chocolate chips
- 1/2 cup granulated sugar
- 1/3 cup vegetable oil
- 1 large egg
- 1 teaspoon vanilla extract
- 1 ½ cups all-purpose flour
- 1 teaspoon baking soda
- 1/2 teaspoon salt
- 1 cup warm water not hot
Instructions
- Preheat oven to 350 F. Grease or line 16 standard muffin tin cups. Set aside.
- To make the filling, beat the cream cheese, sugar, egg, and salt together until well-combined.
- Stir in the mini chocolate chips.
- Set aside.
- Melt the 1/2 cup semisweet chocolate chips over hot, not boiling, water, stirring until smooth.
- Remove from heat and set aside.
- In a large bowl, stir sugar, oil, egg, and vanilla together until well-combined.
- Stir in melted chocolate chips.
- Add flour, baking soda, and salt. Stir in just until combined.
- Mix in the warm water just until combined.
- Divide half of the cupcake batter between the muffin tin cups.
- Drop a rounded tablespoon of filling in each muffin tin cup.
- Top with the remaining half batter.
- Bake for 20-25 minutes.
- Cool in pan for 5 minutes.
- Remove to wire cooling rack to finish cooling.
Video
Notes
- Cream cheese: I’ve used full-fat and reduced-fat cream cheese in this recipe. However, I don’t recommend fat-free cream cheese.
- Mini chocolate chips: I like to use mini chocolate chips in the filling because they don’t sink the way that regular-sized chocolate chips can. You can use regular-sized chocolate chips if you prefer.
- Water: The water should be about 80F. Cold water is more difficult to mix in, and the water should not be boiling water.
- Nutrition values are estimates.
Nutrition
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Adapted from Nestle.
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Comments & Reviews
Julie says
Love these cupcakes!
Kate says
Thank you!
Mary Jane says
One of the best cupcakes ever! I’ll make them again and again.
Lisa says
These are so good! I ate three as soon as they were cool enough to handle:) One of my favorite cupcakes ever.
Kate says
Thank you! I’m so glad that you liked them!
Francine says
Can this recipe be made with gluten free flour
Kate says
I haven’t tried making a gluten-free version to say for certain.