If you’ve ever dreamed of a delightful crossover between rich cheesecake and soft, fluffy muffins, look no further than these Cheesecake Chocolate Chip Muffins. Bursting with flavor and featuring a creamy cheesecake filling, these muffins are an irresistible treat for breakfast, dessert, or any time you need a little indulgence. The combination of chocolate chips and a creamy center makes each bite heavenly. Trust us; these will quickly become a favorite in your home!
Top Reasons to Make Cheesecake Chocolate Chip Muffins

- Decadent Flavor: The blend of chocolate and cheesecake creates a unique taste experience that is hard to resist.
- Easy to Make: With simple steps and ingredients, even novice bakers can whip these up in no time.
- Perfect for Any Occasion: Whether it’s a brunch gathering or an afternoon snack, these muffins are sure to impress.
- Freezable: Make a big batch and freeze them for a quick treat later!
Your Shopping Guide
- 8 oz cream cheese: Ensure it’s softened for easy mixing.
- ½ cup granulated sugar: Sweetens the cheesecake filling.
- 1 large egg: Room temperature for better incorporation.
- ½ tsp vanilla extract: For flavor enhancement in the cheesecake.
- ¼ cup mini chocolate chips: Adds sweetness to the cheesecake filling.
- 2 cups all-purpose flour: The base of the muffin batter.
- ½ cup unsweetened cocoa powder: Gives the muffins their rich chocolate flavor.
- 1 tsp baking soda: For leavening the muffins.
- 1 tsp salt: Enhances overall flavor.
- ½ cup coconut oil: Use warmed to a liquid state for moisture.
- 1 cup granulated sugar: Sweetens the muffin batter.
- 1 large egg: Room temperature for a fluffier texture.
- 1 cup plain Greek yogurt: Adds moisture and a slight tang.
- ¼ cup milk: For a perfect batter consistency.
- ¼ cup strong coffee: Cold, to enhance the chocolate flavor.
- 1 tsp vanilla extract: Adds depth to the muffin batter.
- ¾ cup mini chocolate chips: Divided for both the batter and the filling.
Tools & Equipment Needed
- Mixing Bowls: For combining the ingredients.
- Electric Mixer: To beat the cream cheese and sugar smoothly.
- Measuring Cups and Spoons: For accurate ingredient measurements.
- Spatula: To fold in ingredients gently.
- Muffin Tin: For baking the muffins; use liners for easy cleanup.
- Cooling Rack: To cool the muffins after baking.
Cheesecake Chocolate Chip Muffins, Made Easy

Step 1: Prepare the Cream Cheese Filling
In a medium bowl, beat together the softened cream cheese, ½ cup granulated sugar, 1 egg, ½ tsp vanilla extract, and ¼ cup mini chocolate chips until smooth and creamy. Set aside.
Step 2: Preheat Your Oven
Preheat your oven to 350°F (175°C) and line a muffin tin with paper liners. This ensures your muffins won’t stick and makes for easy serving.
Step 3: Mix the Dry Ingredients
In a large bowl, whisk together 2 cups all-purpose flour, ½ cup unsweetened cocoa powder, 1 tsp baking soda, and 1 tsp salt until well combined.
Step 4: Combine the Wet Ingredients
In another bowl, combine ½ cup melted coconut oil, 1 cup granulated sugar, 1 large egg, 1 cup plain Greek yogurt, ¼ cup milk, ¼ cup cold strong coffee, and 1 tsp vanilla extract. Whisk until the mixture is smooth and well-blended.
Step 5: Combine Wet and Dry Ingredients
Gradually add the wet mixture to the dry ingredients, stirring gently until just combined. Be careful not to overmix; a few lumps are okay.
Step 6: Fold in Chocolate Chips
Gently fold in ¾ cup of mini chocolate chips into the muffin batter. This adds delightful chocolatey goodness to every bite.
Step 7: Fill the Muffin Tin
Spoon a dollop of muffin batter into each muffin cup, filling them about halfway. Then, add a spoonful of the cream cheese mixture on top, followed by more muffin batter to cover the filling. Aim for about ¾ full in total.
Step 8: Bake
Bake in the preheated oven for 18-20 minutes, or until a toothpick inserted into the center comes out clean (a few crumbs are okay, but it should not be wet).
Step 9: Cool
Once baked, remove the muffins from the oven and let them cool in the pan for about 5 minutes before transferring them to a cooling rack to cool completely.
In-Season Flavor Ideas

- Fall: Add a pinch of pumpkin spice to the muffin batter for a seasonal twist.
- Winter: Incorporate peppermint extract into the cream cheese filling for a holiday flavor.
- Spring: Mix in some lemon zest for a bright, refreshing taste.
- Summer: Add fresh berries to the batter for a fruity explosion.
Learn from These Mistakes
- Don’t skip the room temperature eggs and cream cheese; they blend better into the batter.
- Avoid overmixing the batter, as this can lead to dense muffins.
- Be mindful of baking time; muffins can easily overbake and become dry.
- Make sure to let the muffins cool completely before storing to avoid sogginess.
How to Store & Reheat
These Cheesecake Chocolate Chip Muffins can be stored in an airtight container at room temperature for up to 3 days. For longer storage, place them in the refrigerator for up to a week. To reheat, simply pop them in the microwave for about 10-15 seconds or warm them in the oven at 350°F (175°C) for 5-7 minutes.
Questions People Ask
Can I freeze these muffins?
Absolutely! These muffins freeze beautifully. Just place them in a freezer-safe bag or container, and they will keep for up to 3 months. Thaw them in the fridge overnight before enjoying.
Can I substitute Greek yogurt in this recipe?
Yes! You can use sour cream or even a non-dairy yogurt alternative if you prefer. Just ensure it has a similar consistency for the best results.
What can I use instead of coconut oil?
You can substitute the coconut oil with melted butter or another vegetable oil if desired. Just make sure it’s in a liquid state when you add it to the batter.
How can I make these muffins gluten-free?
To make these muffins gluten-free, substitute the all-purpose flour with a 1:1 gluten-free flour blend. Ensure the other ingredients are also gluten-free.
What to Make After This
- Chocolate Chip Banana Bread
- Lemon Blueberry Muffins
- Peanut Butter Chocolate Chip Cookies
- Carrot Cake Muffins
Bring It to the Table
Gather your friends and family for a delightful snack or dessert with these Cheesecake Chocolate Chip Muffins. Their rich flavors and soft textures will make everyone fall in love at first bite. Whether you’re serving them at a brunch or enjoying them with your morning coffee, these muffins are sure to be a hit.
So, roll up your sleeves and dive into this delicious recipe. You’ll be rewarded with a batch of muffins that not only satisfy your sweet tooth but also make you feel like a baking superstar! Enjoy your baking adventure!

Cheesecake Chocolate Chip Muffins
Ingredients
For the Cream Cheese Filling:
- 8 oz cream cheese softened
- ½ cup granulated sugar for filling
- 1 large egg room temperature
- ½ tsp vanilla extract for filling
- ¼ cup mini chocolate chips for filling
For the Muffin Batter:
- 2 cups all-purpose flour
- ½ cup unsweetened cocoa powder
- 1 tsp baking soda
- 1 tsp salt
- ½ cup coconut oil melted
- 1 cup granulated sugar for batter
- 1 large egg room temperature
- 1 cup plain Greek yogurt
- ¼ cup milk
- ¼ cup strong coffee cold
- 1 tsp vanilla extract for batter
- ¾ cup mini chocolate chips divided
Instructions
Instructions
- Step 1: Prepare the Cream Cheese Filling. In a medium bowl, beat together the softened cream cheese, ½ cup granulated sugar, 1 egg, ½ tsp vanilla extract, and ¼ cup mini chocolate chips until smooth and creamy. Set aside.
- Step 2: Preheat Your Oven. Preheat your oven to 350°F (175°C) and line a muffin tin with paper liners.
- Step 3: Mix the Dry Ingredients. In a large bowl, whisk together 2 cups all-purpose flour, ½ cup unsweetened cocoa powder, 1 tsp baking soda, and 1 tsp salt until well combined.
- Step 4: Combine the Wet Ingredients. In another bowl, combine ½ cup melted coconut oil, 1 cup granulated sugar, 1 large egg, 1 cup plain Greek yogurt, ¼ cup milk, ¼ cup cold strong coffee, and 1 tsp vanilla extract. Whisk until smooth.
- Step 5: Combine Wet and Dry Ingredients. Gradually add the wet mixture to the dry ingredients, stirring gently until just combined.
- Step 6: Fold in Chocolate Chips. Gently fold in ¾ cup of mini chocolate chips into the muffin batter.
- Step 7: Fill the Muffin Tin. Spoon a dollop of muffin batter into each muffin cup, filling them about halfway. Then, add a spoonful of the cream cheese mixture on top, followed by more muffin batter to cover.
- Step 8: Bake. Bake in the preheated oven for 18-20 minutes, or until a toothpick comes out clean.
- Step 9: Cool. Let the muffins cool in the pan for about 5 minutes before transferring to a cooling rack.
Equipment
- Mixing bowls
- Electric Mixer
- Measuring cups and spoons
- Spatula
- Muffin Tin
- Cooling rack
Notes
- Store muffins in an airtight container at room temperature for up to 3 days.
- Freeze muffins for up to 3 months; thaw overnight in the fridge.
- Use room temperature ingredients for better mixing.
