Cheesecake Chocolate Chip Muffins

These mouthwatering Cheesecake Chocolate Chip Muffins combine the classic flavors of a Black Bottom Cupcake or Black Bottom Muffins with creamy cheesecake.

Using ingredients such as soft cream cheese, Greek yogurt instead of sour cream, and chocolate chips, these "muffin-meets-cupcake" creations will make everyday feel like a special occasion.

An easy breakfast idea which can also be served as a dessert.

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 as an easy dessert. 

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

If you love chocolate and cheesecake, try my Chocolate Cheesecake Cupcakes!

Looking for more Cheesecake Recipes? Try my Cheesecake Chocolate Chip Muffins, Chocolate Bliss Cheesecake or my Cheesecake Stuffed Strawberries...Yum!

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Main Ingredients Needed

Be sure to see the recipe card for exact quantities, detailed instructions and special notes.

• Unsweetened cocoa powder
• All purpose flour
• Baking soda
• Salt
• Butter
• Granulated sugar
• Eggs
• Plain Greek yogurt
• Milk
• Cooled coffee
• Vanilla extract
• Mini chocolate chips
• 8 oz cream cheese – softened

Step-by-Step Instructions

Step 1 | Prepare the Batters

• Prepare the cheesecake filling and then prepare the chocolate muffin batter.
• Place both batters into separate decorating bags.

Step 2 | How to Fill the Muffin Pan

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

Step 3 | Baking Instructions

• Then top with more chocolate muffin batter.
• Finally, top with a sprinkle of chocolate chips. The liners should be about ¾ of the way full.
• Bake in a preheated 400°F oven for just 5 minutes, then turn the heat down to 350 degrees and continue baking for about 13-15 minutes.
• Cool before unwrapping, the muffins will release better when cooled.

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 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.

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📖 Recipe Card

Lois

Cheesecake Chocolate Chip Muffins

4.63 from 8 votes

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.

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Prep Time 30 minutes mins

Cook Time 20 minutes mins

Total Time 50 minutes mins

Servings: 16 muffins

Course: Breakfast

Cuisine: American

Calories: 315

Ingredients Equipment Method Nutrition

Ingredients

  

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Chocolate Muffin Ingredients

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

Cheesecake Filling Ingredients

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

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Equipment

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

Method

 

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 tablespoon 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.

Nutrition

Serving: 1ServingCalories: 315kcalCarbohydrates: 41gProtein: 6gFat: 15gSaturated Fat: 9gPolyunsaturated Fat: 5gCholesterol: 54mgSodium: 289mgFiber: 2gSugar: 26g

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This recipe has been updated since it first appeared in 2019 with new photos, information and a new printable recipe card that includes nutritional information. I hope you enjoy the updates as much as I enjoyed working on them!