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Pumpkin protein muffins on a cooling rack with a muffin served on the side with tea

Pumpkin Protein Muffins (Low Carb/Keto)

Delicious gluten-free, dairy-free and Paleo-friendly Pumpkin muffins that give you a generous dose of protein without excess calories.
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Course: Breakfast, Snack
Cuisine: American
Keyword: dairy-free, Gluten Free, Paleo, protein
Prep Time: 1 hour
Cook Time: 40 minutes
Servings: 12 muffins
Calories: 270kcal


  • Food processor or stick blender
  • Muffin/cupcake tray (either standard or jumbo)
  • Baking sheet/tray
  • Digital scales
  • Measuring spoons and cups


  • 580 grams (1.27 pounds) Japanese pumpkin (Kabocha squash) puree (Start with 1kg/2lb. raw pumpkin sold as large wedges)
  • 8 extra large eggs
  • 7 teaspoons coconut oil, melted
  • 3 teaspoons vanilla extract
  • 210 grams fine coconut flour (1 ½ cups)
  • 2 teaspoons gluten free baking powder (for strict Paleo, replace the baking powder with 1 teaspoon cream of tartar and ½ teaspoon baking soda)
  • 1 teaspoon cooking salt
  • 90 grams collagen peptides powder (3.2 ounces) (approx. 1 cup minus 1 ½ tablespoons)


  • 75 grams chocolate chips (⅓ cup)
  • 70 grams roasted hazelnut pieces (½ cup)
  • 1 punnet raspberries or blueberries


  • 2 teaspoons ground cinnamon or Pumpkin pie spice


Roast the pumpkin

  • Roast the pumpkin wedges at 200C/390F for 45 minutes a few hours or the day before you want to make the muffins. Check for doneness by inserting a sharp knife - it should go through the flesh easily.
    Drain thoroughly of water before using - there may be a lot of water to drain off, depending. I recommend letting them sit a few hours before draining.
    Weigh out the 580g/1.27 pounds of pumpkin flesh.

Preparing the muffins/pre-heating the oven

  • Pre-heat the oven to 200C/390F.
  • Add the wet ingredients and pumpkin to the food processor and blend for a minute or two. Then add in all of the dry ingredients and blend again. The batter is thicker than other muffin batters.
  • Mix in your choice of mix-ins such as choc chips, berries, chopped nuts. You may want to reserve some for the top.
  • Portion the batter into muffin liners - you will need 12 standard liners or 6 jumbo liners

Bake the muffins

  • Bake for 20 minutes at 200C/390F, then reduce the temperature to 180C/350F. Remove the pan from the oven, loosely tent with foil (optional if you want to avoid too much browning on top) and turn the tray around. Bake for a final 20 minutes or 25 minutes for the jumbo size.
  • Remove the muffins from the oven and lift on to the cooling rack. Allow to cool for half hour before eating and cool completely before refrigerating. Will keep in the fridge for up to 5 days or two months in the freezer.


Serving: 1muffin | Calories: 270kcal | Carbohydrates: 15g | Protein: 15g | Fat: 11g | Sodium: 251mg | Potassium: 64mg | Fiber: 9g