Skip to content

Subscribe for our FREE 30 minute meals book!

  • Recipes
    • Appetizers & Sides
    • Breakfast
    • Desserts
    • Drinks
    • Lunch & Dinner
    • Noodles & Stir Fries
    • Pasta
    • Salads
    • Snacks
    • Soups & Stews
    • Browse All
  • Dinner
  • Dessert
    • Cakes & Cupcakes
    • Chocolate
    • Cookies
  • Diet
    • Egg Free
    • High Protein
    • Nut Free
    • Paleo
    • Refined Sugar Free
    • Vegan
    • Vegetarian
    • Browse All
  • About
    • About Claire
    • Work With Me
    • Recipe Ebook
  • Shop
    • Appetizers & Sides
    • Breakfast
    • Desserts
    • Drinks
    • Lunch & Dinner
    • Noodles & Stir Fries
    • Pasta
    • Salads
    • Snacks
    • Soups & Stews
    • Browse All
  • Dinner
    • Cakes & Cupcakes
    • Chocolate
    • Cookies
    • Egg Free
    • High Protein
    • Nut Free
    • Paleo
    • Refined Sugar Free
    • Vegan
    • Vegetarian
    • Browse All
    • About Claire
    • Work With Me
    • Recipe Ebook
  • Shop

Meal Type ยป Gluten Free Snack Recipes ยป Pumpkin Protein Muffins

Pumpkin Protein Muffins

Claire Cary

By

Claire Cary

No ratings yet
Published: October 16, 2026
Jump to Recipe

These pumpkin protein muffins are a one bowl, easy to make Fall treat with 10 grams of protein per serving. They’re naturally gluten free, perfectly sweet and bursting with fresh Fall spices.

pumpkin protein muffins with chocolate chips on top

My banana protein muffins are still such a popular recipe, so I though it was about time to make a fun Fall variation! These pumpkin protein muffins are the perfect healthier mid day pick me up and take just about 15 minutes of active prep time.

Protein powder is great for baking because it can help turn a very sugar and carb filled recipe into a very nutritious one! These muffins have about 10 grams of protein per serving thanks to the eggs, greek yogurt and protein powder. I usually don’t recommend adding in protein powder to a standard baked good, so it’s key to start with a recipe that already calls for it!

They don’t have an overly protein powdery flavor, but still make sure to choose a protein powder you like the taste of as the flavor naturally does come through. If you love this recipe, try my protein cookie dough or protein overnight oats next!

Quick tips before we bake!

  • I used a vanilla pea protein powder, but you can definitely use a whey protein powder. I don’t recommend a plain protein powder for the best flavor, but if you have a cinnamon or pumpkin spice flavored protein, that would also be delicious!
  • I opted for mini chocolate chips here, but you can opt to omit those and add some chopped nuts or top with a cinnamon streusel that you can find in my classic gluten free pumpkin muffins.
ingredients for the recipe in bowls with labels

Key ingredients

Eggs. You need three whole eggs in this recipe which will help bind all ingredients together and ensure the muffins rise properly. I do not recommend any swaps here- the eggs are key for the protein content and to yield a fluffy texture

Greek yogurt. I love using greek yogurt in baking because it’s such an easy way to add both moisture and protein! To make these dairy free, I suggest the Kite Hill Greek Style yogurt.

Flour. A mix of almond flour and gluten free all purpose flour will keep these gluten free! To make them nut free, just swap the almond flour with an additional 1/4 cup gluten free flour.

Protein powder. I used a vanilla pea protein, which I recommend. I do not suggest chocolate or plain for the best flavor. Same with my banana bread protein cookies!

Sweetener. I used a mix of honey and brown sugar to sweeten these muffins. You can swap the brown sugar for coconut sugar or even just leave that out for a lower sugar option. I do not recommend swapping or omitting the honey.

wet ingredients mixed in a bowl
batter in a glass bowl before resting

How to make protein pumpkin muffins

Preheat the oven to 375 degrees Fahrenheit (not 350!). Line a 12 cavity muffin tin with liners AND spray with oil. I find with protein powder desserts, the batter can get a bit sticky and the liner will peel off more easily if sprayed.

WANT TO SAVE THIS RECIPE?

Enter your email below & we’ll send it straight to your inbox. Plus you’ll get great new recipes from us every week!

In a medium mixing bowl, whisk together the wet ingredients until smooth. Whisk in the dry ingredients. Be sure to spoon and level the flour to measure. Fold in the chocolate chips. Let the batter rest for about 10 minutes.

batter in the muffin tin before baking

Spoon into the prepared muffin tin, filling each pretty much to the top. This will help give nice big muffin tops! Top with extra chocolate chips and/or brown sugar as desired.

Bake for 20-25 minutes or until a toothpick comes out clean. Let cool for 15 minutes, then transfer to a wire rack to finish cooling. Enjoy and try my blueberry protein muffins next!

bite taken out of the muffin to show texture

How to store and freeze

To store: Once prepared, these pumpkin protein muffins will keep at room temperature for about 3 days. I like to store them in a container or a ziplock bag to keep them moist.

To freeze: I have not tried freezing them, but I do think that would work well! Be sure to let them cool completely, then transfer to a freezer safe bag and freeze for up to 1 month. I like to freeze without the wrapper just to make reheating a bit easier.

To reheat: If frozen, let the muffins defrost in the fridge, then reheat until warm through the center at 300. If they were simply in the fridge or at room temperature, just microwave for a few seconds to warm up- especially key if you added chocolate chips!

angled view of the protein pumpkin muffins with chocolate chips

Pumpkin recipes to try next!

  • Baked Pumpkin Oatmeal
  • Vegan Pumpkin Spice Latte
  • Oat Flour Pumpkin Bread

If you want more recipes straight to your inbox, be sure to subscribe to my email list. As always, tag me on instagram if you make this recipe so I can see your creation!

No ratings yet

Pumpkin Protein Muffins

by: claire cary

These pumpkin protein muffins are a one bowl, easy to make Fall treat with 10 grams of protein per serving. They’re naturally gluten free, perfectly sweet and bursting with fresh Fall spices.
/ /
Prep: 15 minutes mins
Cook: 20 minutes mins
Rest Time 10 minutes mins
Total: 45 minutes mins
12

Ingredients

Wet

  • 1 cup pumpkin puree
  • 3 eggs
  • ½ cup greek yogurt
  • ¼ cup honey
  • 1 teaspoon vanilla
  • 2 tablespoons brown sugar

Dry

  • ½ cup almond flour
  • 1 ¼ cups gluten free all purpose 1:1 baking flour
  • ½ cup vanilla protein powder I used pea protein
  • 2 teaspoon baking powder
  • 2 ½ teaspoon pumpkin pie spice
  • ½ teaspoon cinnamon
  • ¼ teaspoon salt
  • ⅔ cup chocolate chips
US Customary – Metric

Instructions

  • Preheat the oven to 375 degrees Fahrenheit (not 350!). Line a 12 cavity muffin tin with liners AND spray with oil. I find with protein powder desserts, the batter can get a bit sticky and the liner will peel off more easily if sprayed.
  • In a medium mixing bowl, whisk together the wet ingredients until smooth. Whisk in the dry ingredients. Be sure to spoon and level the flour to measure. Fold in the chocolate chips. Let the batter rest for about 10 minutes.
  • Spoon into the prepared muffin tin, filling each pretty much to the top. This will help give nice big muffin tops! Top with extra chocolate chips and/or brown sugar as desired.
  • Bake for 20-25 minutes or until a toothpick comes out clean. Let cool for 15 minutes, then transfer to a wire rack to finish cooling. Enjoy!

Notes

If you don’t want to use almond flour, you can swap for an additional 1/4 cup of GF all purpose baking flour.
I used a vanilla pea protein powder, but you can definitely use a whey protein powder. I don’t recommend a plain protein powder for the best flavor, but if you have a cinnamon or pumpkin spice flavored protein, that would also be delicious!
Serving: 1muffin / Calories: 195kcal / Carbohydrates: 28g / Protein: 10g / Fat: 7g / Saturated Fat: 2g / Polyunsaturated Fat: 0.3g / Monounsaturated Fat: 0.5g / Trans Fat: 0.02g / Cholesterol: 52mg / Sodium: 158mg / Potassium: 98mg / Fiber: 3g / Sugar: 16g / Vitamin A: 3261IU / Vitamin C: 1mg / Calcium: 119mg / Iron: 1mg

Did you make this?

Mention @eatwithclarity or tag #eatwithclarity!

leave a comment and rating Cancel reply

Your email address will not be published. Required fields are marked *

Recipe Rating




Comments

claire cary

Welcome,
I’m Claire

Eat With Clarity is a place for gluten free recipes that are just as good as the real thing. With plenty of vegan, vegetarian and paleo options, there is something here for everyone!


Read Claire’s Story

you’ll also love

  • Gluten Free Snack Recipes

    Gluten Free Banana Chocolate Chip Muffins

  • Gluten Free Breakfast Recipes

    Banana Oatmeal Breakfast Cookies

  • gluten free chocolate chip muffins with a bite taken out
    Gluten Free Snack Recipes

    Gluten Free Chocolate Chip Muffins

  • Refined Sugar Free Recipes

    Protein Banana Bread

  • Egg Free Recipes

    Chocolate Protein Pudding

  • Gluten Free Snack Recipes

    Chocolate Chip Greek Yogurt Muffins

claire cary of eat with clarity

get more clarity

"โœฆ" indicates required fields


More

  • About
  • eBook
  • Disclaimer
  • Privacy
  • Services

Recipes

  • Recipe Index
  • Breakfast
  • Desserts
  • Dinner
  • Drinks

As Seen In

  • Buzzfeed
  • Yahoo!
  • Well + Good
  • Parade
  • Self

Site by Katelyn Gambler & Made To Thrive

COPYRIGHT ยฉ 2021 ยท EAT WITH CLARITY, LLC. ALL RIGHTS RESERVED.

Information from your device can be used to personalize your ad experience.

Rate This Recipe

Your vote:




A rating is required
A name is required
An email is required