Warm spices, a boost of vanilla protein, and cozy pumpkin make these gluten-free pumpkin protein muffins the perfect grab-and-go breakfast or snack. They’re ultra soft, filling, and naturally sweetened for cozy Fall days.
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Gluten-Free Protein Pumpkin Muffins
Soft, spiced, and naturally sweet, these protein-packed pumpkin muffins are the kind of treat you’ll want on repeat all season. They’re gluten-free, fluffy, and lightly sweetened with coconut sugar, making them just right for a quick breakfast, snack, or even a healthier dessert. With the addition of vanilla protein powder, they’re as nourishing as they are delicious.
Ingredients and Estimated Cost:
Here is a list of everything you need to make these muffins, along with a few substitution recommendations.
- 2 large eggs – Binds the ingredients together.
- ¼ cup coconut oil – Keeps the muffins soft. Use avocado oil or light olive oil as an alternative.
- 1 15-oz can of pumpkin puree – Adds a natural sweetness with the classic pumpkin flavor.
- 1 teaspoon almond extract – You can use pure vanilla extract or maple extract as an alternative.
- ½ cup coconut sugar – Use light brown sugar for a similar taste.
- 1 ¾ cup gluten-free all-purpose flour – The base of the muffins. You can use regular flour, but the muffins will no longer be gluten-free.
- ½ cup vanilla protein powder – Adds a boost of protein to your diet. Use any protein powder flavor of your choosing, but it will affect the overall taste.
- 1 teaspoon cinnamon – Enhances the pumpkin flavor. Pumpkin pie spice is a good substitute.
- ½ tsp kosher salt – Enhances the overall flavor profile. You can also use sea salt.
- 2 tsp baking powder – Helps the muffins rise and become fluffy.
NOTE: The recipe prices are calculated by using grocery store websites. The actual cost of the recipe will vary depending on what ingredients you already have.
How To Make Protein Pumpkin Muffins
Mix the wet and dry ingredients together, fill the muffin tins, bake, and serve. Let me show you how:
- Mix the wet ingredients. In a large mixing bowl, whisk together the eggs, melted coconut oil, pumpkin puree, and almond extract until smooth.
- Add the dry ingredients and rest the batter. Add the coconut sugar, gluten-free flour, protein powder, cinnamon, salt, and baking powder directly into the wet mixture. Stir with a spatula until just combined. The batter will be thick. Let the batter sit at room temperature for 10 minutes. This allows the flour to hydrate and helps the muffins rise better.
- Fill the muffin cups. Line a 12-cup muffin pan with paper liners. Using a 3-tablespoon scoop, divide the batter evenly among the prepared muffin cups, filling each about ¾ full.
- Bake. Bake in a 425°F preheated oven for 10 minutes. Without opening the oven, reduce the heat to 350°F and continue baking for another 10 minutes, or until the muffins are domed, golden, and a toothpick inserted in the center comes out clean.
- Cool and serve. Let the muffins cool in the pan for 5 minutes, then transfer them to a wire rack to cool completely. Serve.
Optional Mix-ins:
You can make these pumpkin protein muffins with 1 cup of the mix-ins below. Note that adding mix-ins will give 1-2 extra muffins.
- Mini chocolate chips – Rich, melty pockets that pair perfectly with pumpkin.
- Dried cranberries – Tart and chewy, perfect for a festive fall touch.
- Chopped dates – Natural sweetness and caramel notes.
- Chopped toasted pecans – Buttery crunch that’s classic with pumpkin.
- Chopped toasted walnuts – Earthy and hearty, great for texture.
- Pumpkin seeds (pepitas) – Stay crunchy when baked and keep the pumpkin theme going.
Top Recipe Tips
Use room-temperature eggs so the batter mixes evenly.
Rest the batter for 10 minutes before baking—this small step makes a big difference in muffin rise.
Start baking at 425°F to create bakery-style domed tops, then lower the heat to bake the centers through without drying them out.
Protein Pumpkin Muffins
Recipe Cost 11.69 Serving Cost 0.83
Recipe Cost $ 11.69 Serving Cost $ 0.83Ingredients
WET INGREDIENTS:
- 2 large eggs at room temperature
- ¼ cup coconut oil
- 15- oz can of pumpkin puree
- 1 teaspoon almond extract
DRY INGREDIENTS:
- ½ cup coconut sugar
- 1 ¾ cup gluten-free all-purpose flour
- ½ cup vanilla protein powder
- 1 teaspoon cinnamon
- ½ tsp kosher salt
- 2 tsp baking powder
Instructions
Preheat the oven
- Adjust the oven rack to the center position and preheat to 425°F. Line a muffin pan with paper liners.
Mix the wet ingredients
- In a large mixing bowl, whisk together the eggs, melted coconut oil, pumpkin puree, and almond extract until smooth.
Add the dry ingredients
- Add the coconut sugar, gluten-free flour, protein powder, cinnamon, salt, and baking powder directly into the wet mixture. Stir gently with a spatula until just combined. The batter will be thick—don’t overmix.
Rest the batter
- Let the batter sit on the counter for 10 minutes. This helps the flour hydrate and gives the muffins a better rise.
Fill the muffin pan
- Using a 3-tablespoon scoop, divide the batter evenly among the prepared muffin cups, filling each about ¾ full.
Bake
- Bake at 425°F for 10 minutes. Without opening the oven, reduce the temperature to 350°F and continue baking for another 10 minutes, or until the muffins are domed and golden and a toothpick inserted in the center comes out clean.
Cool
- Allow the muffins to cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.
Notes
Equipment
Nutrition
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Protein Pumpkin Muffin Recipe FAQs
These are a great make-ahead option. I like to make them over the weekend and stick them in the refrigerator for quick grabs throughout the week.
The initial 425°F helps the muffins rise. Then you drop the temperature to finish baking the muffins without drying them out.
Just be sure to use a dairy-free protein powder and do not substitute the coconut oil. Everything else is naturally dairy-free in the ingredient list.
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- Gluten-Free Pumpkin Muffins with Orange
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