Go Back
+ servings
Almond flour pumpkin muffins with cream cheese swirl scattered on parchment paper.
Print Recipe
5 from 16 votes

Almond Flour Pumpkin Muffins

These delicious almond flour pumpkin muffins say "fall" with every bite! They're moist and soft with a cream cheese swirled top and loads of pumpkin flavor. Naturally gluten free and can easily be made dairy free too!
Prep Time15 mins
Cook Time15 mins
Total Time30 mins
Course: Muffins
Cuisine: American
Keyword: Almond Flour Pumpkin Muffins, gluten free pumpkin muffins, pumpkin almond flour muffins
Servings: 12 Muffins
Calories: 208kcal


  • 2 eggs
  • 1 teaspoon vanilla extract
  • 1 cup pumpkin puree
  • ¼ cup almond butter
  • cup coconut sugar
  • 1 tablespoon apple cider vinegar
  • 2 cups almond flour
  • ¼ cup tapioca flour
  • 1 teaspoon baking soda
  • ½ teaspoon baking powder

For the cream cheese swirl

  • 5 oz cream cheese - softened and at room temperature
  • 3 tablespoon sugar
  • 1 egg yolk - at room temperature


  • Preheat oven to 375 F. In a large bowl, mix together the eggs, vanilla, pumpkin puree, almond butter, coconut sugar, and apple cider vinegar until well combined with a hand or stand mixer or stiff whisk.
  • Fold in the almond flour, tapioca flour, baking powder, and baking soda until no flour clumps remain. Set the bowl aside.
  • In a separate bowl, beat the cream cheese with the sugar and egg yolk until smooth and creamy.
  • Line a muffin pan with liners and scoop the muffin batter into each liner, filling it about ¾ of the way full. Use a ½ tablespoon to place a dollop of the cream cheese filling on top of each muffin. Then use a toothpick or thin knife to swirl the cream cheese into the muffin batter. This doesn’t need to be perfect. Simply swirl to distribute the cream cheese to the edges of the muffin and down into the middle.
  • Bake the muffins in the oven for 15 - 18 minutes until they have risen and the cream cheese on top has turned a beige color and looks set. Let the muffins cool slightly for no more than 5 minutes before transferring them to a cooling rack. This is important! Don’t leave the muffins in the hot pan for too long or you will end up with soggy and wet muffin bottoms. Sprinkle a little coarse cane sugar on top of the muffins if desired and enjoy!


Storing : Place the cooled muffins in an air-tight container and store out on the counter for up to 4 days or in the fridge for up to a week (my preferred method). You can also freeze the muffins in a freezer bag or airtight container for up to 3 months. Simply thaw the muffins out on the counter or in the fridge until soft.


Calories: 208kcal | Carbohydrates: 20g | Protein: 6g | Fat: 13g | Saturated Fat: 1g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 2g | Trans Fat: 0.003g | Cholesterol: 27mg | Sodium: 138mg | Potassium: 93mg | Fiber: 3g | Sugar: 11g | Vitamin A: 3217IU | Vitamin C: 1mg | Calcium: 77mg | Iron: 1mg