Chocolate Cheesecake Muffins

Name: Chocolate Cheesecake Muffins
Prep time: 25 min
Cook time: 20 min
Total time: 105 min
Ingredients: 8 ounces cream cheese (room temperature); ½ cup granulated sugar; 1 large egg; ½ teaspoon vanilla extract; ¼ cup mini chocolate chips; ½ cup butter (room temperature); 1 cup granulated sugar; 1 large egg; 1 cup plain Greek yogurt; ½ cup whole milk; ¼ cup dark coffee (cooled to room temperature); 1 teaspoon vanilla extract; 2 cups all-purpose flour; ½ cup unsweetened cocoa powder; 1 teaspoon baking soda; 1 teaspoon salt; ¾ cup mini chocolate chips (divided)

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Sink your teeth into delicious chocolate cheesecake muffins perfect for breakfast, brunch or dessert. Your guests will melt for these decadent muffins cheesecake filled chocolate muffins.

Chocolate cheesecake muffins with a marbled chocolate and vanilla interior, one partially unwrapped and missing a bite, sitting on brown parchment paper.

These coffee-flavored chocolate muffins are a perfectly moist quick bread with a filling of chocolate chip cheesecake on the inside.

Ingredients for Chocolate Cheesecake Muffins

This recipe is made in two different steps. Mixing the chocolate cheesecake batter, and mixing the chocolate muffins. Then you put the two together in muffin tins and bake them at the same time.

Ingredients for baking chocolate cheesecake muffins: flour, butter, eggs, Greek yogurt, cocoa powder, granulated sugar, cream cheese, chocolate chips, salt, baking soda, vanilla extract, coffee, and milk.

See the recipe card at the bottom of the post for all ingredients and quantities.

Ingredients for the Chocolate Chip Cheesecake Batter

Cream Cheese.
Granulated Sugar.
Large Egg.
Vanilla Extract.
Mini Chocolate Chips.

Ingredients for the Chocolate Muffins

Butter.
Granulated Sugar.
Large Egg.
Plain Greek Yogurt.
Whole Milk.
Dark Coffee.
Vanilla Extract.
All-Purpose Flour.
Unsweetened Cocoa Powder.
Baking Soda.
Salt.
Mini Chocolate Chips.

Substitutions and Variations

You can substitute the greek yogurt with sour cream.
the dark coffee can be substituted out with water and instant coffee granules or just plain water.
Use whatever kind of chocolate chips you would like in these muffins. You may need to cut a larger hole in the piping bag to get them to pass through though.

NOTE: This recipe has not been tested with other substitutions or variations

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How to Make Chocolate Cheesecake Muffins

Making these beautiful breakfast muffins is not nearly as difficult as it sounds. Your just going to mix up two different batters, and then add them to the muffin liners in a specific order. You’ll end up with chocolate on the outside and cheesecake on the inside. Let your guests be surprised, or spill the beans. You decide.

Before you start mixing the batters, preheat your oven and get out the cupcake liners so that your muffin pans are ready to go.

Making the Cheesecake Batter

Split image: Left shows chocolate chip cannoli filling in a mixing bowl with a spatula. Right shows the filling, perfect for topping chocolate cheesecake muffins, transferred into a piping bag, ready for use.

Step 1: Beat the cream cheese until it is smooth. Add the sugar and mix thoroughly, then add the egg and vanilla and mix it all again really well. Fold in the chocolate chips.

Step 2: Load the resulting batter into a disposable piping bag and place this in the refrigerator to chill while you make the muffin mix.

Making the Chocolate Muffin Mix

Step-by-step baking process: flour and cocoa powder being whisked in a bowl (3), chocolate cheesecake muffins dough mixed in a bowl (4), and chocolate mixture in a piping bag (5).

Step 3: Whisk together the dry ingredients and set aside.

Step 4: Cream the butter and sugar together in a separate large mixing bowl. Mix in the egg, yogurt, milk, coffee and vanilla.

Beat the dry ingredients into the wet on low speed. This is going to result in a very thick batter. Fold in half of the chocolate chips.

Step 5: Scoop the muffin batter into a second disposable piping bag.

Assembling the Chocolate Cheesecake Muffins

Discover how to make chocolate cheesecake muffins in four steps: hollow the center, add creamy white filling, top with dough and chocolate chips, then admire a tray of perfectly finished treats.

Step 6: Cut the tip off of each piping bag. Pipe a ring around the bottom of each cupcake liner with the chocolate batter.

Step 7: Next, pipe about 2 tablespoons of cheesecake batter on top of the ring of chocolate muffin batter.

Step 8 & 9: Top off the muffins with more chocolate batter until 3/4 full. Sprinkle mini chocolate chips on top of each muffin. Bake the muffins according to the instructions on the recipe card and then make sure to cool them completely before removing them from the pan and refrigerating them.

Five chocolate cheesecake muffins are arranged on parchment paper and a red polka dot cloth, with one muffin lying on its side to show its wrapper.

Tips For Best Results

Make sure to cool these muffins completely before storing them in the refrigerator. The muffins will release better from the liners when cooled completely.
Cut more of the tip off of the chocolate batter, which needs to come out in larger quantity. You want the whole to be about the size of a nickel. For the cheesecake batter, cut a smaller amount off the tip, but you want to open it up enough to squeeze mini chocolate chips through the opening.
Several things need to be room temperature for this recipe. Be sure to set out the butter and cream cheese several hours before you plan to bake.

How to Store and Freeze

Keep your leftover muffins in an airtight container or a sealed storage bag in the refrigerator for up to 4 days.

You can also freeze them in an airtight freezer-safe container or sealed freezer bag. They will keep for up to 3 months and can be eaten partially frozen or thawed in the refrigerator overnight.

Recipe FAQs

Is the chocolate muffin batter supposed to be so thick?

Yes. It is a very thick batter and you will have to work to get the mini chocolate chips fully incorporated into this batter. That’s how thick it is.

How long does it take to make chocolate cheesecake muffins?

It will take about 25 minutes to mix up the recipe and assemble the muffin batter. It takes about 20 minutes of baking time as you reduce the oven temperature. The finished muffins should be cooled completely and chilled before serving for best results. Make them the day before and you will be golden!