Cheesecake Chocolate Chip Muffins

Cheesecake Chocolate Chip Muffins takes two of my favorite flavors and combines them into one delicious breakfast muffin that can also be served as dessert. Check out this easy recipe for a delicious, moist, homemade muffin…or maybe it’s a cupcake? You decide! 

Cheesecake Chocolate Chip Muffins are a delicious combination of cheesecake and chocolate cake all in one little package called a muffin. Therefore, they are definitely sweet enough to serve at the end of a meal or place on a dessert buffet table if you’re celebrating something special. 

Cheesecake Chocolate Chip Muffins

This recipe is very similar to a Black Bottom Cupcake or Black Bottom Muffins. However, I’m calling them cheesecake chocolate chip muffins because cheesecake and me are really good friends. It’s actually one of my all-time favorite desserts. 

The chocolate cake portion of this muffin calls for Greek yogurt, but you can definitely substitute sour cream if that’s what you have on hand. 

Tips for Baking Muffins

• Spray the cupcake liners with non-stick cooking spray to make sure the muffin doesn’t stick. I started doing this years ago when the paper liners were sticking to whatever I was baking. 
• I always bake muffins or cupcakes on the center rack in my oven. 
• If for some reason, the muffin pan is not completely filled with muffin batter, fill the empty cups in the pan with water. 
• Always follow baking time directions, but you’ll know when the muffins are done when you insert a toothpick into the center of the muffin and it comes out clean or with just a few crumbs sticking to it. If you have batter sticking to the toothpick, you need to bake them for a few extra minutes. 

How to Make Cheesecake Chocolate Chip Muffins

Make sure you print out the recipe below and save it for later!

Preheat oven to 400 degrees. Prepare two muffin pans with liners. This recipe should yield about 16 muffins depending on the size of your muffin pan and how full you fill them. 

Chocolate Muffin Ingredients

• ½ cup unsweetened cocoa powder
• 2 cups all purpose flour
• 1 tsp baking soda
• 1 tsp salt
• 1 stick – unsalted butter
• 1 cup granulated sugar
• 1 egg
• 1 cup plain Greek yogurt
• ½ cup milk
• ¼ cup cooled coffee
• 1 tsp vanilla extract
• ¾ cup mini chocolate chips

Cheesecake Filling Ingredients

• 8 oz cream cheese – softened
• ½ cup granulated sugar
• 1 egg
• ½ tsp vanilla extract
• ¼ cup mini chocolate chips

How to Prepare the Cheesecake Filling:

1. In a medium bowl, mix the cream cheese and sugar until creamy.
2. Add in the egg and vanilla extract, continue mixing until well combined.
3. Gently mix in the chocolate chips.
4. Take a large Ziploc bag or piping bag and spoon the cheese cake filling into the bag.
5. Chill in the fridge until needed.

How to Prepare the Chocolate Muffins:

1. In a large bowl, combine the dry ingredients: flour, cocoa powder, baking soda and salt. Set aside.
2. In another bowl, beat the butter and sugar until creamy.
3. Then, add in the egg, yogurt, milk, coffee and vanilla.
4. Mix well until everything is well combined.
5. Slowly, add in the dry ingredients into the wet and mix until everything is well combined.
6. Gently mix in ½ of your chocolate chips.
7. Take a large Ziploc bag or piping bag and spoon the batter into your bag. The batter will be very thick.
8. Cut the tips off of your bags and squeeze about a tbsp. of muffin batter into the muffin liners.
9. Then, squeeze about 2 tbsp of cheesecake batter on top and top with more muffin batter.
10. Finally, top with a sprinkle of chocolate chips.
11. The liners should be about ¾ of the way full.

Let’s Get Baking! 

To begin with, prepare the cheesecake filling and then prepare the chocolate muffin batter. Yes, you’ll have to clean the mixing bowl after the cheesecake filling, but that’s okay. However, these muffins are worth the extra dish washing you have to do! 

How to Fill Plastic Decorating Bags

Here’s an easy tip I’ve shared before on how to fill the plastic decorating bags: 

• Take a large plastic storage bag or a disposable decorating bag, and place it inside a large drinking glass or tall jar. 
• Cuff the excess bag over the sides of the glass. 
• Make sure the inside of the bag is smooth by pressing it to the sides of the drinking glass. 
• Spoon the batter into the bag using a spatula being careful not to fill it all the way up or the batter will overflow once you start squeezing. 
• Gently lift the bag out of the glass jar and squeeze it gently to work the batter down into the bottom of the bag. 
• Twist the end of the bag and snip one corner with the kitchen scissors.

How to Fill the Muffin Pan:

1. Cut the tips off of your bags and squeeze about a tbsp. of muffin batter into the muffin liners.
2. Then, squeeze about 2 tbsp of cheesecake batter on top. Then top with more muffin batter.
3. Finally, top with a sprinkle of chocolate chips. The liners should be about ¾ of the way full.

Squeeze some of the cheesecake filling on top of the chocolate muffin batter. 

Next cover with another swirl of the chocolate muffin batter followed by a few extra chocolate chips. I really like using mini chocolate chips for this recipe. But if all you have are regular size chocolate chips on hand…go for it! 

How to Bake the Muffins:

1. Bake at 400 for just 5 minutes, then turn the heat down to 350 degrees and continue baking for about 13-15 minutes.
2. Cool before unwrapping, the muffins will release better when cooled.

Cheesecake Chocolate Chip Muffins takes two of my favorite flavors and combines them into one delicious breakfast muffin that can also be served as dessert. All that's missing is a cup of coffee or tea!

More Delicious Chocolate Recipes

• Chocolate Chunk Muffins
• My Favorite Recipe for Chocolate Cheesecake
• Chocolate Brownie Cake with Homemade Chocolate Ganache

Cheesecake Chocolate Chip Muffins

Yield: 16 muffins

Prep Time: 30 minutes

Cook Time: 20 minutes

Total Time: 50 minutes

Cheesecake Chocolate Chip Muffins takes two of my favorite flavors and combines them into one delicious breakfast muffin that can also be served as dessert.

Print

Ingredients

Chocolate Muffin Ingredients

• 2 cups all purpose flour
• ½ cup unsweetened cocoa powder
• 1 tsp baking soda
• 1 tsp salt
• 1 stick – unsalted butter
• 1 cup granulated sugar
• 1 egg
• 1 cup plain Greek yogurt
• ½ cup milk
• ¼ cup cooled coffee
• 1 tsp vanilla extract
• ¾ cup mini chocolate chips

Cheesecake Filling Ingredients

• 8 oz cream cheese – softened
• ½ cup granulated sugar
• 1 egg
• ½ tsp vanilla extract
• ¼ cup mini chocolate chips

Instructions

HOW TO PREPARE THE CHEESECAKE FILLING:

1. In a medium bowl, mix the cream cheese and sugar until creamy.
2. Add in the egg and vanilla extract, continue mixing until well combined.
3. Gently mix in the chocolate chips.
4. Take a large Ziploc bag or piping bag and spoon the cheese cake filling into the bag.
5. Chill in the fridge until needed.

HOW TO PREPARE THE CHOCOLATE MUFFINS:

1. In a large bowl, combine the dry ingredients: flour, cocoa powder, baking soda and salt. Set aside.
2. In another bowl, beat the butter and sugar until creamy.
3. Then, add in the egg, yogurt, milk, coffee and vanilla.
4. Mix well until everything is well combined.
5. Slowly, add in the dry ingredients into the wet and mix until everything is well combined.
6. Gently mix in ½ of your chocolate chips.

HOW TO FILL THE MUFFIN PANS:

1. Take a large Ziploc bag or piping bag and spoon the batter into your bag. The batter will be very thick.
2. Cut the tips off of your bags and squeeze about a tbsp. of muffin batter into the muffin liners.
3. Then, squeeze about 2 tbsp of cheesecake batter on top and top with more muffin batter.
4. Finally, top with a sprinkle of chocolate chips.
5. The liners should be about ¾ of the way full.

HOW TO BAKE THE MUFFINS:

1. Bake at 400 for just 5 minutes, then turn the heat down to 350 degrees and continue baking for about 13-15 minutes.
2. Cool before unwrapping, the muffins will release better when cooled.

Recommended Products

As an Amazon Associate and member of other affiliate programs, I earn from qualifying purchases.

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  Large Disposable Icing Decorating Bags Cake Piping Bags with 5 Bag Ties
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  Wilton Elegance Cupcake Liners, 150-Count
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  AmazonBasics Nonstick Carbon Steel Muffin Pan - 2-Pack

Nutrition Information:

Yield: 16 Serving Size: 1
Amount Per Serving: Calories: 315Total Fat: 15gSaturated Fat: 9gTrans Fat: 0gUnsaturated Fat: 5gCholesterol: 54mgSodium: 289mgCarbohydrates: 41gFiber: 2gSugar: 26gProtein: 6g

The nutrition information is calculated automatically. I cannot guarantee its accuracy. If this data is important to you, please verify with your trusted nutrition calculator.