Cheesecake Chocolate Chip Muffins

Two of my favorite flavors combine into one delicious Cheesecake Chocolate Chip Muffins. Another easy breakfast idea which can also be served as a dessert.

This recipe is very similar to a Black Bottom Cupcake or Black Bottom Muffins. Get ready to see how to make this homemade muffin from scratch!

this Recipe

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. 

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. 

Table of Contents

• Helpful Kitchen Tools
• Main Ingredients Needed
• Step-by-Step Instructions
• Tips for Baking Muffins
• How to Fill Plastic Decorating Bags
• Cheesecake Chocolate Chip Muffins

Helpful Kitchen Tools

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Main Ingredients Needed

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

• Unsweetened cocoa powder
• Aurpose 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.

Tried any of my recipes? Let me know in the comments!

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.

More Delicious Chocolate Recipes

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

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!