Pumpkin Protein Muffins Recipe (Gluten-Free)

Kid-friendly pumpkin protein muffins that are light, fluffy, and moist! The perfect quick and healthy fall breakfast that your family will love! Gluten-free and easy to make dairy-free or vegan.

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Jump to:

• Why You Have to Make These Muffins!
• Ingredients You Need for This Recipe
• How to Make This Recipe
• How to Store Pumpkin Muffins
• Expert Tips
• Recipe FAQs
• Related Recipes
• Pumpkin Protein Muffins Recipe (Gluten-Free)

It's the time of year to bake all of the pumpkin treats! When the fall season hits, healthy pumpkin desserts and pumpkin spice breakfast recipes are our favorite.

As if you couldn't get enough, pumpkin for breakfast is also a thing with these overnight oats! Or if you're here because muffins are your thing, be sure to check out all of the healthy muffin recipes here including easy pumpkin banana muffins, copycat Starbucks pumpkin muffins, or these protein blueberry muffins!

Why You Have to Make These Muffins!

• Great protein muffin recipe for kids and toddlers!
• A perfect make-ahead snack that freezes well.
• Healthy pumpkin muffins are quick to prep and bake - just like these protein bars with pumpkin!
• Easy to make a double batch for an easy and quick breakfast or healthy snack.
• Delicious pumpkin protein muffins have the perfect amount of sweetness from maple syrup and a bit of chocolate.
• Added protein from the protein powder - get inspo from these protein pumpkin recipes.
• Dairy-free and gluten-free!
• Easy to make vegan.
• A great option to use up extra pumpkin puree.
• This protein muffin recipe is made with no refined sugar!
• Try these almond flour banana muffins or lemon protein muffins with blueberries for another healthy breakfast.
• Try healthy pumpkin cheesecake and healthy pumpkin pie for another fall treat.

Ingredients You Need for This Recipe

Here are the ingredients you need to make this recipe. Reference the recipe card at the bottom for exact measurements and the notes below for substitution ideas.

Wet Ingredients

Canned pumpkin puree is one of the base ingredients of protein pumpkin muffins. It provides color, flavor, moisture, and texture.

Use canned pumpkin, not pumpkin pie filling. You can generally find canned pumpkin in the baking section or the canned vegetables section of your grocer.

Fresh pumpkin puree can be used.

Maple syrup sweetens this recipe without adding refined sugars. You can sweeten it using brown sugar, honey, or coconut sugar.

Eggs provide structure, binding, and moisture. To make this recipe vegan or eggless, you can use unsweetened applesauce or flax eggs.

Vanilla extract adds a warm flavor.

Coconut oil adds a fat component, helping the muffins to be moist. Use refined coconut oil to remove the coconut flavor.

Greek yogurt has been added to the ingredients to increase the protein. Use plant-based Greek yogurt like Kite Hill to make it dairy-free.

Dry Ingredients

Mini dark chocolate chips are my favorite and add a bit of sweetness. Chopped almonds, pecans, or walnuts would also work.

Vegan vanilla protein powder provides extra protein. Whey protein powder can be used.

Cinnamon provides a warm spice. Pumpkin pie spice also works.

Salt helps to balance the sweetness of the other ingredients.

Baking soda and baking powder are necessary baking ingredients that help the muffins to rise.

How to Make This Recipe

Below are step-by-step instructions for how to cook this recipe. The recipe card at the bottom shows the exact cooking time and temperatures.

Step 1

Line a muffin tin with muffin liners or silicone baking cups. Spray the baking cups with nonstick spray or coconut oil spray.

Add the dry ingredients to a large mixing bowl and whisk them until incorporated.

Step 2

In a separate medium bowl, mix together wet ingredients until the mixture resembles a creamy pumpkin pie texture.

Step 3

Combine the wet with the dry ingredients and fold in any mix-ins and stir until just moistened. Do not overmix.

Step 4

Use a standard-sized cookie scoop to scoop out 10-12 muffins. Bake at 425F for 5 minutes and 350F for 10-15 minutes or until a toothpick comes out clean.

How to Store Pumpkin Muffins

Allow muffins to cool completely and then store them in an airtight container at room temperature for up to 2 days or up to 5 days in the refrigerator.

To freeze, allow the muffins to cool completely. Then, wrap them individually in plastic wrap or place them in a freezer-safe container.

Allow the muffins to thaw at room temperature or reheat them in the microwave.

Expert Tips

• If the muffin batter seems too thick, add 1 tablespoon of almond milk to moisten. Add more if needed.
• Depending on the protein powder used, the sweetness may need to be adjusted.
• Spray muffin liners with coconut oil spray or use silicone baking cups for easy removal.
• Allow healthy pumpkin protein muffins to cool completely before peeling the muffin liners.
• Top with some almond butter or peanut butter!
• To make these in one bowl, try these blender muffins, and just swap bananas for pumpkin.
• Try these pumpkin protein bars for another healthy pumpkin protein snack!

Recipe FAQs

Related Recipes

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