Gluten Free Pumpkin Muffins (High Protein)

If you love starting your morning with something soft, fluffy, and packed with autumn flavor, these Gluten Free Pumpkin Muffins (High Protein) are the very best treat! They're bursting with cozy spices, earthy pumpkin, and just the right touch of sweetness—all while delivering a serious protein punch.

What makes these muffins a must-try? They're made with wholesome ingredients, naturally gluten free flours, and a secret boost of protein from Greek yogurt and protein powder. You get bakery-style texture with none of the gluten and all the goodness you crave.

Perfect for meal prepping your breakfasts, satisfying snack cravings, or fueling your post-workout hunger, these muffins are a staple in my kitchen every fall. You’ll be amazed how easy they are to make—no fancy equipment needed!

Bake a batch for your next brunch, or keep them on hand for busy mornings. Once you try them, you’ll never go back to bland breakfast bars again!

Why You'll Love This Recipe

• Deliciously moist and fluffy—no dry or dense gluten free muffins here!
• High in protein, so they keep you satisfied longer and make a great on-the-go breakfast.
• Naturally gluten free and made with wholesome ingredients, so everyone can enjoy.
• Incredibly easy to make with simple prep and minimal cleanup.
• Perfect for meal prep—they freeze and reheat beautifully!

Key Ingredients for Gluten Free Pumpkin Muffins (High Protein)

See recipe card below for full list of measurements, ingredients, and instructions.

Pumpkin Puree

Pumpkin puree is the star of these muffins, giving them their rich, moist texture and classic fall flavor. Make sure to use pure pumpkin puree (not pumpkin pie filling) for the best results. Canned or homemade both work, but canned is super convenient and reliable. If needed, sweet potato puree can be swapped in for a slightly different but equally delicious result.

Gluten Free Oat Flour

Oat flour makes these muffins light and tender while keeping them completely gluten free. You can buy certified gluten free oat flour or make your own by blending rolled oats in a food processor until fine. If you’re out of oat flour, almond flour can be substituted, but the texture will be a little more dense and nutty.

Vanilla Protein Powder

This is the secret to turning your muffins into a high-protein powerhouse! Choose your favorite gluten free vanilla protein powder for a little sweetness and plenty of protein. If you’d rather skip the protein powder, just add an extra ¼ cup of oat flour, but the protein boost is what sets these muffins apart.

Greek Yogurt

Greek yogurt adds moisture, a slight tang, and a big protein lift to the batter. Use plain, unsweetened Greek yogurt for the best control over flavor and sweetness. Dairy free? Substitute a plant-based Greek-style yogurt—just make sure it’s thick and unsweetened.

Pumpkin Spice

A mix of cinnamon, nutmeg, ginger, and cloves brings that classic pumpkin spice warmth to every bite. If you don’t have pumpkin spice blend, you can mix your own using ground cinnamon, ginger, nutmeg, and cloves in the proportions you love.

Instructions for Gluten Free Pumpkin Muffins (High Protein)

See recipe card below for full list of measurements, ingredients, and instructions.

Preheat and Prep Your Muffin Tin

Start by preheating your oven to 350°F (175°C). Line a 12-cup muffin tin with parchment liners or lightly grease with oil to prevent sticking.

Mix the Wet Ingredients

In a large bowl, whisk together the pumpkin puree, eggs, Greek yogurt, coconut sugar, melted coconut oil, and vanilla extract until smooth and creamy. Be sure the coconut oil isn’t hot, or it may cook the eggs!

Combine the Dry Ingredients

In a separate bowl, stir together the oat flour, protein powder, baking soda, baking powder, pumpkin spice blend, and salt. Mix well so the leavening and spices are evenly distributed.

Bring It All Together

Add the dry ingredients to the wet mixture. Gently fold with a spatula until just combined—be careful not to overmix, or your muffins could turn out dense. If you’re using chocolate chips or nuts, fold those in now.

Fill and Bake

Divide the batter evenly among the muffin cups, filling each about 3/4 full. Bake for 22-25 minutes, or until the tops are set and a toothpick inserted in the center comes out clean or with just a few moist crumbs.

Cool and Enjoy

Let the muffins cool in the tin for 5 minutes, then transfer to a wire rack to cool completely. Enjoy warm or at room temperature!

Recipe Variations

Make Them Dairy Free

For a fully dairy free batch, simply use a plant-based Greek-style yogurt. You can also use dairy free chocolate chips or skip the mix-ins altogether.

Chocolate Pumpkin Protein Muffins

Add 2 tablespoons of unsweetened cocoa powder to the dry ingredients and swap chocolate chips for extra-decadent chocolate pumpkin protein muffins.

Nutty Crunch

Fold in 1/3 cup chopped pecans, walnuts, or sunflower seeds for added crunch and healthy fats. You can also sprinkle extra nuts on top for a pretty, bakery-style finish.

Lower Sugar Option

To reduce sugar, substitute a granulated zero-calorie sweetener or cut the coconut sugar to 1/4 cup. The muffins will still have plenty of flavor from the pumpkin and spices.

Add Fruit

Gently fold in 1/2 cup fresh blueberries or diced apples for a fruity twist. Just be aware that extra moisture from the fruit may slightly alter baking time.

Serving Suggestions

Enjoy your Gluten Free Pumpkin Muffins (High Protein) with a dollop of Greek yogurt and a sprinkle of cinnamon for breakfast, or pair them with a hot mug of coffee or tea as a cozy afternoon snack. For a heartier meal, serve alongside scrambled eggs or a smoothie. Garnish with extra pumpkin seeds, a drizzle of nut butter, or a handful of mini chocolate chips for an extra treat.

Storage and Reheating

Store leftover muffins in an airtight container at room temperature for up to 2 days, or in the fridge for up to 5 days. To reheat, microwave on high for 15-20 seconds to restore that just-baked softness. For longer storage, freeze muffins for up to 3 months—just thaw overnight in the fridge or pop in the microwave straight from the freezer for a quick breakfast on the go.

Frequently Asked Questions About Gluten Free Pumpkin Muffins (High Protein) (FAQ)

Q: Can I use almond flour instead of oat flour?
A: Yes, you can use almond flour, but the texture will be a bit denser and the muffins will have a slight nutty flavor. You may need to add an extra tablespoon since almond flour absorbs less liquid.

Q: What type of protein powder works best?
A: Any gluten free vanilla protein powder works well, including whey or plant-based varieties. Just make sure it’s a flavor you enjoy and isn’t overly sweetened.

Q: How do I make these muffins vegan?
A: Swap the Greek yogurt for a plant-based version and use flax eggs (2 tablespoons flaxseed meal + 5 tablespoons water) instead of eggs. The texture will be slightly different but still delicious!

Q: Are these muffins kid-friendly?
A: Absolutely! Kids love their soft, fluffy texture and warm pumpkin spice flavor. You can even add mini chocolate chips for extra appeal.

These Gluten Free Pumpkin Muffins (High Protein) are the perfect way to kickstart your day with flavor, nourishment, and a touch of fall coziness. I hope you love them as much as I do—don’t forget to leave a comment or rate the recipe if you give them a try!