Home » Black Bottom Cupcakes With Mini Chocolate Chips

Black Bottom Cupcakes With Mini Chocolate Chips

Name: Black Bottom Cupcakes With Mini Chocolate Chips
Prep time: 15 min
Cook time: 16 min
Total time: 36 min
Yield: 12
Cuisine: American
Ingredients: 1 cup flour; 1/2 cup white sugar for cake batter + 1/3 cup for cream cheese filling; 1/4 cup unsweetened cocoa powder; 3/4 teaspoon baking soda; 1/2 teaspoon salt; 1/2 cup milk; 1/4 cup vegetable oil; 1/2 teaspoon white vinegar; 1 teaspoon vanilla extract; 8 ounces cream cheese - at room temperature; 1 large egg - at room temperature; 1/2 cup mini chocolate chips

Laura @ Join me in the Kitchen

July 23, 2025

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Group of black bottom cupcakes and mini chocolate chips on a light gray surface.

Jump to Recipe

Rich, indulgent, and incredibly moist, this chocolate cupcake recipe is perfect for any occasion. The cupcakes have a fudgy chocolate base with a creamy chocolate chip cheesecake center, are easy to make, and are a hit at every gathering.

Prep Time: 15 minutes
Recommended Baking Time: 16 to 20 minutes
Rest Time: 5 minutes
Total Time: 36 minutes
Yields: 12 regular-size cupcakes
Prep Level: Beginner +

What You’ll Love

Flavor Combination – Rich chocolate cupcakes with a cream cheese center perfectly combined for a delicious dessert.
Easy to Make – Made with simple ingredients and ready in about 45 minutes.
Great for All Occasions – Perfect for birthday parties, Valentine’s Day, or any special occasion.

Close up of a black bottom cupcake in a baking pan.

I have been making these chocolate cream cheese cupcakes since high school. It was one of my favorite recipes and one of the first cupcake recipes I baked. Mainly because it was an easy recipe and because they are delicious. Back then, I used a chocolate cake mix. I now know that homemade chocolate cupcakes taste so much better than boxed!

Various sizes of bowls with ingredients for cupcakes: flour, cocoa powder, sugar, mini chocolate chips, milk, vegetable oil, cream cheese, salt, white vinegar, baking soda, vanilla extract, and an egg. Items are on a light gray surface.

Ingredient Notes

White vinegar – Don’t skip the vinegar. When white vinegar and baking soda are combined in the batter, it helps the cupcake batter rise, making for a moist, fluffy texture.
Cream cheese – Be sure to use full-fat cream cheese at room temperature. Cold cream cheese won’t mix well and tends to leave small lumps in the filling.
Chocolate chips – You can use mini chocolate chips or regular chocolate chips. I prefer the miniature chocolate chips, so each delicious bite is filled with chocolate chips. You can use any of your favorite chips, such as dark chocolate, milk chocolate, or semi-sweet.

Step-by-Step Instructions

There is a large white mixing bowl with a flour and dry cocoa mixture in it. There is a whisk resting in the bowl. There is a white cloth napkin and a sifter in the background. Items are on a light gray surface.

There is a white mixing bowl with a light yellow liquid mixture in it. There is a whisk resting in the bowl. There is a large white mixing bowl with a flour and dry cocoa mixture in it. Bowls are on a light gray surface.

There is a large white mixing bowl with a flour, dry cocoa, and liquid mixture in it. There is a whisk resting in the bowl. There is an empty white bowl and a white cloth napkin. Items are on a light gray surface.

There is a large white mixing bowl with a chocolate cupcake mixture in it. There is a whisk resting in the bowl. There is an empty white bowl and a white cloth napkin. Items are on a light gray surface.

Make the chocolate batter

In a large bowl, sift the flour, 1/2 cup sugar, cocoa powder, baking soda, and 1/2 teaspoon salt.
In a medium bowl, add the milk, oil, vinegar, and vanilla extract. Whisk until blended.
Add the wet ingredients to the dry ingredients, and stir until the batter is smooth and well combined.

Large glass mixing bowl with an egg, cream cheese, and sugar in it. There is a metal measuring cup with mini chocolate chips and a white cloth napkin. Items are on a light gray surface.

There is a large clear glass mixing bowl with a light yellow batter in it. There is a hand-held mixer over the bowl. There is a metal measuring cup with mini chocolate chips in it and a white cloth napkin. Items are on a light gray surface.

There is a large clear glass mixing bowl with a light yellow batter in it. There is a mound of mini chocolate chips on top of the batter. There is a light gray rubber spatula laying next to the bowl. There is an empty metal measuring cup and a white cloth napkin. Items are on a light gray surface.

There is a large clear glass mixing bowl with a light yellow cake batter and mini chocolate chips in it. There is a light gray rubber spatula resting in it. There is an empty metal measuring cup and a white cloth napkin. Items are on a light gray surface.

Prepare the cream cheese filling

In a separate bowl, combine the cream cheese, 1/3 cup sugar, egg, and a dash of salt. Beat until smooth.
Fold in the chocolate chips.

There are two cupcake pans with white liners and chocolate batter in them. In the background there is a large clear glass bowl with a cream cheese and chocolate chip mixture in it. There is a scoop utensil resting in the bowl. Items are on a light gray surface.

There are 2 six cup muffin pans with white liners. There is a combination of chocolate batter and a cream cheese with chocolate chips mixture in them. There is an empty owl with a scoop utensil in the background. Items are on a light gray surface.

Assemble the cupcakes

Divide the chocolate cupcake batter evenly among the lined cupcake pans.
Spoon about 1 tablespoon of the cream cheese mixture into the middle of each cupcake.

Bake

Place the muffin tin(s) in the preheated oven and bake until the chocolate cake portion is set and the creamy cheesecake filling is slightly golden.

Nine black bottom cupcakes on a black wire rack. Rack is on a light gray surface.

Cool & Serve

Remove the pan from the oven and allow the cupcakes to cool in the pan for about 5 minutes, then transfer the cupcakes to a wire rack to cool completely.

See the recipe card below for complete measurements and baking time.

Tips & Tricks

Use room temperature cream cheese and egg – they blend smoother and there will be a lesser chance for lumps.
Scoop the chocolate batter first – then gently top with a spoonful of the cream cheese mixture. It will naturally bake into a layered marbled look,
Use cocoa powder, not melted chocolate – it gives a rich chocolate flavor without making the batter too dense.
Let the cupcakes cool completely before serving – the cream cheese layer sets up best at room temperature or slightly chilled.

Storing

Due to the cream cheese, you need to refrigerate the black bottom cupcakes. Store the cupcakes in an airtight container in the refrigerator for up to 5 days.

Group of black bottom cupcakes and mini chocolate chips on a light wood surface.

Make Ahead

These delicious black bottom cupcakes are perfect for making ahead since they stay moist and flavorful. Bake them a day or two before and refrigerate. Bring to room temperature for about 30 minutes before serving.

More delicious sweet treats to try!

Scottish Shortbread
Chocolate Chip Pecan Pie
Easy Bread Pudding with Rum Sauce
Easy Churro Cheesecake Bars
Coffee and Cream Brownies from Cooking with Carlee

Yield: 12