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Close up of a Pumpkin Protein Muffin with the muffin paper pulled down with more muffins in the background.

Fluffy Pumpkin Protein Muffins

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  • Author: Sabrina Russo
  • Total Time: 48 minutes
  • Yield: 1 dozen muffins 1x


 These Pumpkin Protein Muffins get a boost of nutrition with protein powder, and are gluten-free and dairy-free friendly. 


  • 1 ¼ cups all purpose flour or gluten free all-purpose blend
  • 1 teaspoon baking soda
  • ½ teaspoon baking powder
  • ½ teaspoon kosher salt (¼ teaspoon fine salt)
  • 1 teaspoon ground cinnamon
  • ½ teaspoon ground ginger
  • ¼ teaspoon freshly grated nutmeg (or ground)
  • 1/8 teaspoon ground cloves
  • ¾ cup coconut sugar
  • 2 large eggs, at room temperature
  • ½ cup coconut oil
  • ¾ cup canned pumpkin puree
  • ½ cup plain Greek yogurt (full fat or low fat, or vegan alternative), at room temperature
  • 2 teaspoons vanilla extract
  • ½ cup Naked Bone Broth protein powder


  1. Preheat oven and prep pan. If you’re planning to bake the muffins the day you make the batter, heat oven to 425F. Line a standard muffin tin with 12 liners.

  2. Mix the dry ingredients. In a medium sized mixing bowl, whisk together the flour, baking soda, baking powder, salt and ground spices.

  3. Mix the wet ingredients. In a large bowl, whisk together the sugar and eggs until thoroughly mixed. Whisk in the oil. Whisk in the pumpkin, yogurt and vanilla extract.

  4. Make protein paste. Add 2 tablespoons of boiling water to the protein powder, 1 tablespoon at a time. Mix thoroughly to make a smooth paste. Make sure there are no lumps. Whisk protein paste into the wet ingredients.

  5. Combine wet and dry ingredients. Add dry ingredients to wet ingredients in 2-3 additions. Mix until homogenous, but do not overmix.

  6. Let batter rest (optional). For taller, fluffier muffins rest the batter at least an hour or up to overnight in the refrigerator. Preheat oven to 425F when you’re ready to make the muffins.

  7. Bake. Divide muffin batter evenly amongst muffin cups in tin. Bake on the center rack of the oven for 5-7 minutes, or until muffin tops rise about 1/4 inch above the top of the tin. Reduce oven to 350F. Continue to bake for 10-15 minutes or until a toothpick inserted into the center comes out clean. Cool tray on wire rack for 5-10 minutes. Remove muffins from tin and place directly on rack. Cool completely. Enjoy.


Feel free to substitute 1 3/4 teaspoons of pumpkin pie spice for the individual spices.

You can use granulated sugar or a combo of 1/2 cup granulated sugar and 1/4 cup light brown sugar in place of coconut sugar. I do not recommend sugar substitutes.

You can use vegetable oil or light olive oil instead of coconut oil.

Do not use a sweet protein powder instead of the Naked bone broth powder. 

Add chocolate chips or nuts to these muffins, if desired. 

You can freeze cooked and cooled muffins for up to 3 months. I wrap them in plastic and then place them in a ziplock storage bag. Defrost overnight in the fridge before you’re planning to eat them.

  • Prep Time: 30 minutes
  • Cook Time: 18 minutes
  • Category: Muffins
  • Method: Bake
  • Cuisine: American


  • Serving Size: 1 muffin
  • Calories: 220
  • Sugar: 13g
  • Sodium: 193mg
  • Fat: 11g
  • Saturated Fat: 8g
  • Unsaturated Fat: 3g
  • Trans Fat: 0g
  • Carbohydrates: 25g
  • Fiber: 1g
  • Protein: 6g
  • Cholesterol: 33mg