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Low carb pumpkin muffins (keto-friendly)

Low Carb Keto Pumpkin Cream Cheese Muffins

Easy, moist and delicious low carb pumpkin muffins with a cream cheese filling, made using almond flour, coconut flour, and pumpkin pie spice. These keto muffins are also gluten-free.
Course Breakfast, brunch, Dessert
Cuisine American
Diet Gluten Free
Prep Time 10 minutes
Cook Time 20 minutes
Total Time 30 minutes
Servings 12 muffins
Calories 246kcal


  • Silicon baking molds
  • mixing bowls
  • Hand or electric whisk
  • spatula or wooden spoon


Low Carb and Keto Pumpkin Muffins

  • 2 cups blanched almond flour
  • cup coconut flour
  • 1 cup pumpkin puree (homemade or canned. If using canned, make sure it is made from pure pumpkins with no added sugar)
  • 2 teaspoon pumpkin pie spice
  • 1 teaspoon baking powder
  • ½ teaspoon baking soda
  • ½ cup granulated monk fruit sweetener
  • teaspoon salt
  • 1 teaspoon vanilla extract
  • ¼ cup coconut oil (melted then cooled) use refined to avoid strong coconut smell
  • 1 tablespoon psyllium husk (optional)
  • 6 tablespoon almond milk or your favorite plant-based milk
  • 4 medium-sized eggs at room temparature
  • 1 tablespoon apple cider vinegar (or lemon juice)

Cream Cheese Filling

  • 8 ounce cream cheese (about 230 grams)
  • ½ cup powdered monk fruit sweetener
  • 1 teaspoon vanilla extract


Making the Cream Cheese Filling or Frosting

  • In a small bowl and using an electric or hand mixer, beat together cream cheese, powdered monk fruit sweetener, and vanilla extract until creamy and smooth. Cover it with a plastic wrap or cling-film, and keep in it the fridge to chill while you make the muffin batter. You want to keep the frosting as cold as possible, so it stays in the middle and does not spread during baking.

Making the Low Carb Pumpkin Muffin Batter

  • Preheat the oven at 350 degrees F (about 177degrees C).
  • Prepare the muffin tin by greasing it with some melted coconut oil or lining it with muffin liners.
  • Using a medium-sized bowl, combine the dry ingredients - almond flour, coconut flour, pumpkin pie spice, baking powder, baking soda, psyllium husk, granulated monk fruit sweetener, and salt.
  • In another bowl, prepare the wet ingredients by whisking eggs, pumpkin puree, apple cider vinegar, coconut oil, almond milk, and vanilla extract.
  • Slowly add the dry ingredients into the bowl with the wet ingredients and combine properly until you obtain a nice smooth batter. Bear in mind that the dough will be slightly firm, and not as runny.
  • Using an ice-cream scoop or a spoon, fill each muffin liner about halfway with batter. Place some of the frosting in the middle then top again with the rest of the batter. Scoop any leftover cheese filling on top. If you like, use a toothpick to make swirls on the surface. I like to sprinkle some pumpkin pie spice on top, just before popping them in the oven.
  • Bake for about 20-30 minutes or until the tops turn golden brown and a toothpick inserted at the center comes out clean.
  • Serve the keto pumpkin cream cheese muffins with a cup of coffee or tea for breakfast, or enjoy them as a healthy snack.



  • You can make your own pumpkin pie spice by combining 1 teaspoon ground cinnamon, ¼ teaspoon ground nutmeg, ¼ teaspoon ground ginger, and ¼ teaspoon ground cloves.
  • You can use homemade or canned pumpkin puree. If using canned, make sure it is made from pure pumpkins with no added sugar).
There are so many ways to vary these keto cream cheese pumpkin muffins:-
  • Paleo option - make the keto pumpkin muffins paleo-friendly by using paleo cream cheese.
  • Pumpkin seeds - top with some pumpkin seeds just before baking, for a crunchy taste.
  • Streusel topping - make a streusel or crumb topping by combining almond flour, butter, and cinnamon.
  • Chocolate chips - stir in half a cup of unsweetened chocolate chips to the pumpkin muffins batter.
  • The keto and low-carb pumpkin muffins will keep on the countertop for up to 5 days and in the fridge for about one week.
  • Freeze them for 2-3 months by keeping them in a single layer in an airtight container, in the freezer. Also, label any freezing bags or containers used properly with the name, baking date, and the date frozen. To use the frozen muffins, simply allow them to thaw completely on the countertop before using. Simply warm up the thawed muffins in the oven for about 3-5 minutes to give them a freshly baked feel and warmth.


Calories: 246kcal | Carbohydrates: 8g | Protein: 7g | Fat: 22g | Saturated Fat: 9g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 2g | Trans Fat: 1g | Cholesterol: 75mg | Sodium: 198mg | Potassium: 93mg | Fiber: 3g | Sugar: 2g | Vitamin A: 3511IU | Vitamin C: 1mg | Calcium: 105mg | Iron: 1mg