Keto Chocolate Cheesecake Muffins (Dairy-Free)

My Keto Chocolate Cheesecake Muffins are a dream come true. They are made with a decadent chocolate batter, topped with a dairy-free cheesecake batter and filled with dark chocolate chips! These can serve as a sweet treat, dessert or breakfast. Keto, Paleo and Dairy-Free


All diets and lifestyles should include chocolate. It makes life a little sweeter. My new Keto Chocolate Cheesecake Muffins allow you to have your cake and eat it too, but, in a healthy way! These are a great sweet treat dessert, snack, or even breakfast. Eat them hot or straight from the fridge. Both ways are super delicious and satisfying. The best part is they are keto, dairy-free, and Paleo.

Tips for making these Keto Chocolate Cheesecake Muffins

  • Don’t overcook. I like to take them out a minute or two early and let them continue cooking in the muffin tin on he stove. This will allow them to be super moist.
  • As far as a Keto and low-sugar liquid sweetener, I always recommend Monk Fruit Syrup. It doesn’t have a yucky after taste like most Keto sugar substitutes.
  • Don’t eyeball your measurements. Make sure to use measuring cups and spoons to get accurate measurement.
  • For low sugar dark chocolate chips, I use Lily’s for Keto and Hu for Paleo.
  • If you are not living Keto, feel free to sub maple syrup for the Monk Fruit Syrup.
  • Store them in the fridge if you have any leftovers. In my opinion, they are so yummy once they have set in the fridge over night. But, they are also good hot with a big cup of coffee.


If you are lucky enough to have any leftovers, you can store them in the fridge or in the freezer for a later date. These are great right out of the oven, but I have found through experience that they are super yummy straight from the fridge. In addition, if you have a sweet tooth a lot, make a big batch of these and freeze. Once your craving kicks in, grab one from the freezer and heat up. So darn yummy!

Fridge: Store in an air-tight container for up to one week. Eat straight out of the fridge or heat up in the microwave for 15-20 seconds.

Freezer: Store in an air-tight container for up to 3 months. Simply thaw and heat up when ready to enjoy!

The Process:

Shop My Post

Want More Healthy Desserts?

clock clock iconcutlery cutlery iconflag flag iconfolder folder iconinstagram instagram iconpinterest pinterest iconfacebook facebook iconprint print iconsquares squares iconheart heart iconheart solid heart solid icon

Keto Chocolate Cheesecake Muffins

  • Author: Ashley McCrary
  • Prep Time: 10 minutes
  • Cook Time: 25-30 minutes
  • Total Time: 25 minute
  • Yield: 1214 muffins 1x
  • Diet: Gluten Free


My Keto Chocolate Cheesecake Muffins are a dream come true. They are made with a decadent chocolate batter, topped with a dairy-free cheesecake batter and filled with dark chocolate chips! These can serve as a sweet treat, dessert or breakfast. Keto, Paleo and Dairy-Free



Dry Ingredients:

  • 1 1/2 cups blanched almond flour
  • 3 tbsp coconut flour
  • 1/4 tsp salt
  • 1 1/2 teaspoon gluten-free baking powder 
  • 3/4 cup dark chocolate chips*
  • 1/2 cup  unsweetened cocoa powder

Wet Ingredients:

  • 3 large eggs (at room temperature)
  • 3/4 cup Monk Fruit Syrup (for Paleo, sub Honey or Maple Syrup)
  • 1 tsp pure vanilla extract
  • 1/2 cup unsweetened almond milk
  • 1/3 cup melted ghee or coconut oil

Cheesecake Topping


  1. Preheat the oven to 350°F and line a cupcake pan with 12 paper liners.
  2. In a medium bowl, whisk together the cocoa powder, almond flour, coconut flour, baking powder, and salt.
  3. In a large bowl, whisk together the eggs, pure vanilla, almond milk, Monk Fruit Syrup (or Maple Syrup) and melted ghee. Use a rubber spatula to fold the dry ingredients into the wet ingredients in ¼-cup increments. Fold in the chocolate chips.
  4. Place the ingredients for the cheesecake mixture into a medium bowl and whip using a handheld mixer. Mix for 30-40 seconds or until smooth. 
  5. Spoon the chocolate batter evenly into the paper liners. Fill about 3/4 of each liner with batter. To the top of the batter, add about a tablespoon of the cheesecake mixture. Swirl together with a fork or a toothpick.
  6. Bake until a toothpick inserted into the center of a muffin comes out clean, 22-25 minutes, or until a toothpick comes out clean. Remove the muffins from the oven and transfer them to a rack and allow to cool in the pan for 5 to 10 minutes.
  7. If leftovers, store in an airtight container. Will last up to 1 week


  • 7.2 NET carbs per muffin
  • For low sugar dark chocolate chips, I use Lily’s for Keto and Hu for Paleo. 
  • Make sure to use either Monk Fruit Syrup or Maple Syrup. If you substitute the granulated Monk Fruit, the batter will become thick and it will not turn out. 
  • If you are not dairy-free, feel free to sub regular cream cheese. 
  • These can be stored in the freezer for up to 3 months.
  • Nutrition is calculated using Monk Fruit Syrup and Lily’s Chocolate Chips.
  • Remember, all ovens cook differently. Be sure to keep an eye on the muffins and cook until a toothpick comes out clean and the muffins are set.
  • Category: Dessert/Snack
  • Method: Oven
  • Cuisine: American

Keywords: Cheesecake Chocolate Muffins, Keto Muffins, Keto, Dairy-Free

Pin These Keto Chocolate Cheesecake Muffins To Pinterest

Keto Chocolate Cheesecake Muffins Pinterest Pin

Comments (3)

  • This recipe looks absolutely delicious. Is there anything I can sub for the coconut cream? Sour cream or more cream cheese maybe?

  • These are THE BEST keto dessert I’ve ever had! I’m usually very disappointed with all keto “sweets”. These are Everything!

    • This is awesome news. I am so happy it was a hit


Write a comment

Recipe rating