Pumpkin Protein Muffins

These high-protein pumpkin muffins are fluffy, soft, and a perfect breakfast or quick snack. They're healthy, gluten-free, and made with protein powder and Greek yogurt. Each muffin has over 10 grams of protein!

Moist pumpkin muffins with protein powder

Pumpkin spice season is my favorite. Ever since I first shared these pumpkin protein muffins back in 2020, they’ve been a hit! They’re that cozy, satisfying treat you can feel great about—packed with warm spices, real pumpkin, and a good dose of protein powder for an extra boost.

These muffins started as a simple idea: I wanted something tasty that could double as a snack or pre-workout fuel. It had to be easy to whip up, but still feel like a treat. After a few tries, they came together perfectly—soft, moist, and loaded with pumpkin flavor. The protein powder and Greek yogurt add that filling factor, so you’re not just getting a sweet snack but a muffin that actually fuels you.

Making them is EASY too. With ingredients like Greek yogurt, protein powder, and canned pumpkin, you’ll have a batch ready in no time. And the best part? You get that delicious pumpkin spice fix with zero guilt because these muffins are secretly healthy.

If you’re looking for more pumpkin treats, our household is also obsessed with pumpkin spice latte baked oatmeal, almond flour pumpkin muffins, and banana pumpkin muffins. But these protein muffins? They’re definitely a new go-to!

Why you'll love this high-protein recipe:

• Protein-Packed: Each pumpkin muffin has 12 grams of protein.
• Simple Ingredients: Made with wholesome, minimal ingredients.
• Quick & Easy to Make: Whip up a batch fast for a grab-and-go snack.
• Perfect for Meal Prep: Bake once, enjoy all week.
• Naturally Sweetened: Coconut sugar and maple syrup add just the right sweetness.
• Gluten-Free & Low-Carb: Made with almond flour and protein powder.
• Cozy Fall Flavors: Pumpkin puree, pumpkin spice, and cinnamon make these muffins a fall favorite.
• Try these healthy oat flour pumpkin muffins or these almond flour pumpkin muffins next!

Ingredients in the recipe

These high-protein pumpkin muffins are made with simple, healthy ingredients. They're fluffy, secretly healthy, and made with protein powder. Here’s what you need:

• Eggs: For texture, rise, and added protein.
• Pumpkin Puree: Use pure pumpkin puree, not pumpkin pie filling.
• Almond Butter: Adds moisture and protein, keeping these muffins oil- and butter-free.
• Greek Yogurt: Adds protein and keeps the muffins soft.
• Milk: Use almond milk or any milk you prefer.
• Maple Syrup: Adds natural sweetness.
• Vanilla Extract: For extra flavor.
• Coconut Sugar: A natural sweetener without refined sugar.
• Almond Flour: Makes the muffins gluten-free and adds healthy fats.
• Protein Powder: Adds extra protein; vanilla or unflavored works best.
• Baking Powder: Helps the muffins rise.
• Pumpkin Pie Spice: For that cozy fall flavor.
• Chocolate Chips: Optional, but a tasty addition!

How to make pumpkin protein muffins

These fluffy and moist pumpkin protein muffins are super easy to make in under 45 minutes. Here’s how to make them:

Step One: First, preheat oven to 350°F and line a cupcake tin with liners.

Step Two: In a large bowl, whisk together the eggs, pumpkin puree, Greek yogurt, almond milk, maple syrup, and coconut sugar. Whisk until there are no clumps.

Step Three: Add the almond flour, protein powder, pumpkin spice, cinnamon, and baking powder. Gently fold until combined. Then, fold in chocolate chips with a spatula.

Step Four: Divide the batter between muffin cups, filling each about two-thirds full. Add extra chocolate chips on top if you like.

Step Five: Bake for 18–20 minutes until a toothpick comes out clean. Let the pumpkin protein muffins cool completely before enjoying them!

Top recipe tips:

1. Room Temperature Ingredients: Let the eggs and Greek yogurt come to room temperature for a smoother batter.
2. Protein Powder Flavor: You can use vanilla, unflavored, snickerdoodle, or pumpkin spice protein powder if needed.
3. Mix-Ins: Add chocolate chips, nuts, or dried fruit for extra flavor and texture.
4. DIY Pumpkin Spice: If you’re out of pumpkin pie spice, make your own with cinnamon, nutmeg, ginger, and cloves.
5. Let Muffins Cool: Allow the muffins to cool completely to help them set. Because they are made with protein powder, cutting them too soon can cause them to fall apart.
6. Make Mini Muffins: Make mini muffins by adjusting bake time to 7–10 minutes.

Easy ingredient substitutions:

• Almond Butter: You can use cashew, sunflower, or peanut butter. Note that peanut butter will change the flavor.
• Greek Yogurt: Substitute with dairy-free yogurt or blended cottage cheese.
• Almond Milk: Any milk or milk alternative will work—try oat, cashew, or cow's milk.
• Maple Syrup: Honey or agave nectar can replace maple syrup.
• Coconut Sugar: You can use brown sugar or granulated sugar instead.
• Protein Powder: Feel free to use your favorite protein powder flavors, like vanilla, pumpkin, coffee, or Snickerdoodle.
• Chocolate Chips: Swap in raisins, dried cranberries, or chopped nuts for a different flavor.

Frequently Asked Questions

Why are my protein muffins dry?

If your protein muffins turn out dry, it could be due to using too much protein powder instead of almond flour. Also, ensure you added the correct amount of Greek yogurt and maple syrup, as both contribute to the muffins' moisture.

Can I use cottage cheese instead of Greek yogurt?

Yes, you can! Just blend the cottage cheese until smooth before using it as a substitute.

Can I use fresh pumpkin instead of canned pumpkin puree?

Yes, you can use fresh pumpkin puree. Just cook and puree a small pumpkin or butternut squash, then drain it well to achieve the right consistency before using it in your recipe.

What's the best type of protein powder to bake with?

I used vanilla whey protein powder for these muffins, but pea protein works well, too! For the best results, choose a plain or vanilla-flavored protein powder.

How can I make these muffins lower in sugar?

You can reduce the amount of maple syrup or use a sugar substitute like stevia or erythritol.

Can I freeze these muffins?

Yes! Freezing muffins is a great option for meal prep. Let the muffins cool to room temperature, then place them in a freezer-safe, airtight bag. You can freeze them for up to 3 months. When you're ready to enjoy one, microwave it for 20 to 40 seconds until warm.

How do I store these muffins?

Store these pumpkin protein muffins in an airtight container at room temperature for 3 days. For longer storage, keep them in the fridge for up to a week or freeze them for up to 3 months.

If you loved this recipe, try these recipes next!

• Nut-Free Protein Bars
• Strawberry Smoothie Bowl
• Best Protein Mug Cake
• Protein Chocolate Chip Baked Oats
• High Protein Acai Bowl
• Best Protein Overnight Oats
• Banana Peach Protein Smoothie

Did you make this recipe?

If you make this recipe, be sure to comment and rate it down below. Also, don't forget to tag me @healthfulblondie on Instagram and use the hashtag #healthfulblondie so I can see your delicious creation and share it with my followers!

📖 Recipe

I only recommend products I love and use myself. In full disclosure, I may receive a small compensation for purchasing a product I recommend. Thank you for supporting Healthful Blondie!

Sharing is caring!