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Healthy Pumpkin Protein Muffins

  • Author: Amy Estes
  • Total Time: 40 minutes
  • Yield: 12 people 1x
  • Diet: Gluten Free


Protein-packed, super moist, and delicious! These Pumpkin Protein Muffins are the perfect mid-afternoon or pre-workout snack to energize you and satisfy that sweet tooth! Gluten-free, refined sugar-free, and refined flour free!


  • 1 cup pumpkin puree (not pumpkin pie filling)
  • 1 cup plain greek yogurt
  • 2 large eggs, lightly whisked
  • 1 tablespoon maple syrup (plus 1 teaspoon )
  • 1 teaspoon vanilla extract
  • 1 1/2 cups blanched almond flour
  • 1 1/2 scoops protein powder (about 2 tablespoons, chocolate, plain, or vanilla work fine)
  • 1 1/2 teaspoons pumpkin pie spice
  • 1 teaspoon ground cinnamon
  • 1 teaspoon baking powder
  • 1/4 teaspoon kosher salt
  • 3/4 cup mini or regular chocolate chips


  1. Preheat oven to 350 degrees F and line a 12-cup muffin pan with muffin liners and lightly spray them with cooking spray. 
  2. Add all of the pumpkin puree, greek yogurt, eggs, maple syrup, and vanilla to a high-speed blender and pulse to combine.
  3. Pour the blended wet ingredients into a mixing bowl and add in the almond flour, protein powder, pumpkin pie spice, ground cinnamon, baking powder, and salt and mix until a smooth batter forms.
  4.  Fold in 2/3 cup of the chocolate chips into the batter – I used mini chocolate chips
  5. Evenly divide the batter between the muffin cups, filling each about ¾ full. Top each with the remaining chocolate chips
  6. Bake in the middle rack of your preheated oven for 30-35 minutes, until the tops are nice and golden brown. 
  7. Remove from the oven, let cool for at least 30 minutes, and enjoy!


  1. To keep the fat down, use nonfat plain greek yogurt. Regular greek yogurt also works.
  2. Use real pumpkin puree, not pumpkin pie filling.
  3. To keep the sugar low in this recipe I used mini sugar-free dark chocolate chips.
  4. Use blanched almond flour and not just pulsed almonds. It literally makes all of the difference. Oat flour also works in this recipe in the same amount as the almond flour.
  5. You can use plain or vanilla protein powder. I have not tried this with chocolate protein powder but I am sure that would also be delicious.
  6. Let the muffins cool completely (at least 30 minutes) before eating since they will stick to the muffin liners if they do not cool enough.
  7. These muffins can be stored for up to 4 days in an airtight container.
  8. For even size muffins use an ice cream scoop to fill the muffin cups with the batter.
  • Prep Time: 5 minutes
  • Cook Time: 35 minutes
  • Category: Breakfast
  • Method: Baking
  • Cuisine: American