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5 from 1 vote

Keto Chocolate Cheesecake Muffins

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
Prep Time10 minutes
Course: Dessert/Snack
Cuisine: American
Diet: Gluten Free
Keyword: Cheesecake Chocolate Muffins, dairy-free, keto, Keto Muffins
Method: Oven
Servings: 12 -14 muffins
Author: Ashley McCrary


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

  • 8 oz dairy-free cream cheese I use Kite Hill
  • 1/4 cup powdered Swerve
  • 2 tablespoons unsweetened canned coconut milk
  • 1 teaspoon vanilla extract


  • Preheat the oven to 350°F and line a cupcake pan with 12 paper liners.
  • In a medium bowl, whisk together the cocoa powder, almond flour, coconut flour, baking powder, and salt.
  • 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.
  • 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. 
  • 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.
  • 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.
  • 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.