Keto Pumpkin Cream Cheese Muffins

Keto Pumpkin Cream Cheese Muffins

The Spruce / Ariane Resnick

Prep: 10 mins
Cook: 20 mins
Total: 30 mins
Servings: 12 servings
Yield: 12 muffins
Nutrition Facts (per serving)
235 Calories
20g Fat
9g Carbs
7g Protein
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Nutrition Facts
Servings: 12
Amount per serving
Calories 235
% Daily Value*
Total Fat 20g 26%
Saturated Fat 5g 23%
Cholesterol 61mg 20%
Sodium 276mg 12%
Total Carbohydrate 9g 3%
Dietary Fiber 3g 11%
Total Sugars 4g
Protein 7g
Vitamin C 1mg 4%
Calcium 151mg 12%
Iron 1mg 8%
Potassium 224mg 5%
*The % Daily Value (DV) tells you how much a nutrient in a food serving contributes to a daily diet. 2,000 calories a day is used for general nutrition advice.
(Nutrition information is calculated using an ingredient database and should be considered an estimate.)

When autumn—aka pumpkin spice season—hits, sweet treats suddenly appear everywhere. If you're trying to eliminate or reduce carbs, that can be a frustrating affair since most are filled with sugar. These keto pumpkin cream cheese muffins will help you say “yes” to choices that are sugar-free, but still wholly delicious, with a bonus that they're so portable. The cream cheese swirl adds lovely richness to the otherwise light and delicate crumb. By using almond flour in place of wheat, grains are eliminated as well as gluten, making these safe for gluten-free eaters.

If you'd like to add an additional homemade element, you can bake your own pumpkin instead of using the canned version. This will result in a thinner puree, so you'll want to add an additional tablespoon or two of coconut flour until the texture feels and looks as thick as a standard muffin batter. Because fresh pumpkin is more yellow and the canned type is more orangey-brown, the color from a homemade puree will be a bit lighter.


For the Cream Cheese Filling:

  • 3/4 cup cream cheese, softened

  • 2 tablespoons non-caloric natural sweetener (such as brown or granular Swerve, allulose, lakanto, or monk fruit)

For the Muffins:

  • 2 cups almond flour

  • 3/4 cup non-caloric natural sweetener (such as brown or granular Swerve, allulose, lakanto, or monk fruit)

  • 1 tablespoon baking powder

  • 1 teaspoon pumpkin pie spice

  • 1/2 teaspoon salt

  • 1 cup pumpkin puree

  • 1/4 cup plain Greek yogurt

  • 1/4 cup neutral oil (such as grapeseed or avocado)

  • 3 eggs

Steps to Make It

  1. Gather the ingredients. Preheat the oven to 375 F.

    Keto Pumpkin Cream Cheese Muffins ingredients

    The Spruce / Ariane Resnick

  2. In a small mixing bowl, whisk cream cheese with the 2 tablespoons of sweetener and set aside.

    whisk cream cheese with sweetener

    The Spruce / Ariane Resnick

  3. Combine the almond flour, 3/4 cup of the sweetener, baking powder, pumpkin pie spice, and salt in a large mixing bowl.

    Mix dry ingredients together

    The Spruce / Ariane Resnick

  4. Add pumpkin puree, yogurt, eggs, and oil, and whisk until a thick batter is formed.

    Add pumpkin puree, yogurt, eggs, and oil

    The Spruce / Ariane Resnick

  5. Divide batter between 12 greased and/or lined muffin tin cups, then place a dollop of cream cheese in each. Stir cream cheese mix with a toothpick to create a swirl in each muffin.

    Divide batter and place a dollop of cream cheese in each

    The Spruce / Ariane Resnick

  6. Bake for 22 minutes, until set and golden.

    Bake keto pumpkin cream cheese muffins

    The Spruce / Ariane Resnick

  7. Let cool for 10 minutes before removing from the pan and serving.

    Remove from pan and enjoy

    The Spruce / Ariane Resnick


  • You can make your own pumpkin pie spice mix if you'd like to have extra on hand for future baking.
  • If there's a particularly spice in pumpkin pie spice mix that you especially love (such as ginger or cinnamon), you can add 1/2 teaspoon of that in addition to the spice mix without offsetting the dry ingredient ratio.
  • These will work with any non caloric sweetener, so choose the one you prefer the taste of. Note that if you use brown Swerve, the color will be slightly darker.
  • Some recipes for these muffins suggest half a cup of butter; we opted for a quarter cup each of Greek yogurt and a neutral oil for more moisture and protein, and less risk of over-browning. If you'd rather use butter, you can substitute those ingredients for half a cup of melted butter. Note that the muffins may brown more quickly.