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Keto Pumpkin Cheesecake Muffins

Soft, sweet pumpkin muffins with a cream cheese filling are baked with coconut flour. Low carb and gluten free.
Prep Time15 mins
Cook Time30 mins
Total Time45 mins
Course: Dessert
Cuisine: Low carb, Vegetarian
Keyword: coconut flour, keto muffins
Servings: 12 muffins
Calories: 181kcal


  • ½ cup butter
  • ½ cup brown monkfruit or other low carb sweetener
  • 4 medium eggs
  • ½ cup coconut flour
  • cup whey protein powder
  • 1 teaspoon baking powder
  • 1 teaspoon vanilla extract
  • 1 teaspoon pumpkin spice
  • ½ cup pumpkin puree canned/tinned
  • ½ teaspoon salt
  • 2 tablespoons almond milk (more may be needed)


Decorations (optional)

  • ¼ cup pumpkin seeds


Make the Filling

  • In a small bowl whisk the cream cheese and sweetener until smooth.

Make the Muffins

  • Preheat the oven to 180C/350F degrees and line a muffin tin with 12 liners.
  • In a medium bowl whisk the butter and low carb sweetener together until smooth.
  • Whisk in the eggs, one at a time until light and fluffy.
  • Add the coconut flour, whey protein powder, baking powder, pumpkin spice, pumpkin puree, vanilla extract, almond milk and salt. Whisk to combine.
  • If the muffin mixture is too thick, add more almond milk.


  • Spoon the pumpkin muffin mixture into the muffin cases.
  • Make a small indentation in the top of the muffin with the back of a spoon for the cream cheese filling.
  • Spoon a large tablespoon of the cream cheese mixture into the indentation and spread it evenly. Add more mixture if there is room.
  • Sprinkle the top with pumpkin seeds.
  • Bake for 25-30 minutes until the muffins are firm and golden brown.


Makes 12 muffins.
The net carbs will be the total carb count minus the fibre count. Carb count excludes sugar alcohols.
Any nutritional analysis on the website is based on an estimate, calculated by Spoonacular from the individual ingredients in each recipe. Variations may occur for various reasons, including product availability and food preparation. We make no representation or warranty of the accuracy of this information.


Serving: 1muffin | Calories: 181kcal | Carbohydrates: 5g | Protein: 6g | Fat: 16g | Fiber: 2g