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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

  • Total Time: 39 minute
  • Yield: 12-14 muffins 1x



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.
  • Author: Ashley McCrary
  • Prep Time: 10 minutes
  • Cook Time: 25-30 minutes
  • Category: Dessert/Snack
  • Method: Oven
  • Cuisine: American
  • Diet: Gluten Free

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