Pumpkin Protein Muffins
Breakfast,  Desserts,  Snacks

Pumpkin Protein Muffins (Flourless & One Bowl!)

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These Healthy Pumpkin Protein Muffins are the best EVER! They are super moist, perfectly tender, and truly the best way to start your day. They also make great snacks. My kids love them! Gluten-free, vegan, & nut-free.

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Yield: 11

Pumpkin Protein Muffins (Flourless + One Bowl!)

Pumpkin Protein Muffins

These Healthy Pumpkin Protein Muffins are the best EVER! They are super moist, perfectly tender, and truly the best way to start your day. They also make great snacks. My kids love them! Gluten-free, vegan, & nut-free.

Prep Time 10 minutes
Cook Time 15 minutes
Total Time 25 minutes



  • 2 flax eggs (2 Tbs. ground flax + 4 Tbs. water. Stir and let thicken for 5 minutes.) or 2 regular eggs
  • 1 cup pumpkin puree
  • ½ cup pure maple syrup (I buy mine in bulk)



1. Preheat oven to 350 F. and grease 11 muffin tins with coconut oil. You may also use paper muffin liners or silicone muffin liners.

2. In a medium bowl add all wet ingredients and mix until smooth. Add in all dry ingredients except baking powder and dark chocolate chips. Mix until smooth and then gently fold in the baking powder and dark chocolate chips until just combined. 

3. Fill 11 muffin tins ¾ full with batter. Top with a few more dark chocolate chips if desired. Bake at 350 F. for 15-18 minutes or until a toothpick comes out with a few moist crumbs. Cool at least 20 minutes in muffin tins. Then carefully twist muffins to loosen them and remove from muffin tins. Enjoy! Store in an airtight container on the counter for up to 5 days, in the refrigerator for up to 8 days, or freeze for up to 3 months.


1. Protein Powder: you can substitute vanilla whey protein powder or really any protein powder you have on hand here. I haven’t tested another protein powder personally, but they should turn out well! You can also try and use ⅓ cup more oat flour in place of the protein powder. Let me know what protein powder you use in the comments so I know it works well if you try 🙂

2. Flax egg: I like grinding my whole flax seeds up in my coffee grinder and then storing them in the freezer. This ensures that you get all the benefits from the freshly ground flax + it stays good for 5+ months in the freezer!

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Nutrition Information:



Amount Per Serving: Calories: 150Total Fat: 4.5gCarbohydrates: 25.4gNet Carbohydrates: 21.8gFiber: 3.6gSugar: 13.2gSugar Alcohols: 0gProtein: 5.8g

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I cannot wait for you to give these easy Healthy Pumpkin Protein Muffins a try! Please snap a picture and share it with me! Seeing your kitchen creations makes my day and encourages me to keep creating new recipes for you!

More Healthy Pumpkin Recipes

Pumpkin Cookie Skillet

Fudgy Zucchini Brownies

Pumpkin Chocolate Chip Cookies

Healthy Pumpkin Chocolate Chip Muffins

Pumpkin Swirl Cheesecake

Pumpkin Bread

gluten free pumpkin protein muffins

Healthy Protein Pumpkin Muffins

If you love a nice moist, fluffy pumpkin muffin, this is the recipe for you. Just like my Healthy Lemon Poppyseed Muffins recipe, or my Healthy Chocolate Chip Pumpkin Muffins, these muffins are secretly healthy, but you would never know. They are perfectly sweetened and absolutely delicious! Read more about what makes these pumpkin muffins “healthy” below! 

Vegan Pumpkin Chocolate Chip Muffins

These pumpkin protein muffins are 100% vegan and egg-free! We use 2 flax eggs instead of regular eggs for this recipe. If you can have eggs though and would prefer to use them, go ahead! The muffins will be amazing either way. And if you’re looking for more healthy vegan recipes, definitely check out my Homemade Chocolate Sauce, Chocolate Crinkle Cookies, Fudgy Zucchini Brownies, and so many more!

healthy pumpkin muffins

High Protein Pumpkin Muffins

Like I said before, you only need one bowl for this healthy pumpkin protein muffin recipe. I hate using multiple bowls for baking. If you feel the same way, then you definitely need to check out my Healthy Baking Course **Use code “SHH20” to get an exclusive 20% off! I teach you all the simple tips and tricks to make healthy baking easy! To make these protein pumpkin muffins you simply mix all the wet ingredients and then all the dry. Fill up your muffin tins and bake! Full instructions are in the recipe above 🙂

What Protein Powder To Use For These Pumpkin Muffins?

This is definitely the most commonly ask question I get. I use this vegan vanilla protein powder. It has clean ingredients and the price point is great. You can also use any protein powder from the company Clean Simple Eats! It’s by far my favorite protein powder EVER! Use code “CLAIRE” to save money on your order too! They actually have a pumpkin pie flavored protein powder that I definitely try in my next batch of these pumpkin protein muffins 🙂 YUUMM!!

flourless protein pumpkin muffins

Gluten-Free Pumpkin Chocolate Chip Protein Muffins

I love creating gluten-free secretly healthy recipes here at the Secretly Healthy Home. You know it’s my jam. And if you know me, you know that I LOVE chocolate everything. So you’re in the right place for gluten-free, pumpkin, and chocolate. If you’ve tried my healthy fudge brownies, pumpkin chocolate chip baked oatmeal, pumpkin cookie skillet, pumpkin chocolate chip cookies, or my no-bake peanut butter pumpkin bars, you know what I’m talking about. This gluten-free pumpkin chocolate chip muffin recipe is no different, my friends!

kid approved healthy muffins

Flourless Pumpkin Protein Muffins

Reasons To Love These Gluten-Free Chocolate Muffins?

  1. Ridiculously easy to make! Just pop everything into a mixing bowl, mix it up, then bake and enjoy!
  2. Perfect amount of fluff and moisture. These gluten-free muffins are fluffy without being too dry or dense. They are perfectly moist!
  3. Flavor explosion. The pumpkin fall flavor + dark chocolate chips is literally a match made in heaven. Plus the added protein is just a benefit!
  4. Super healthy and filling. Since these muffins have healthy ingredients in them, they will keep you fuller longer and won’t spike your blood sugar as badly. Especially because they have the added protein powder. 
  5. High in fiber. Ya gotta love oats for being such an amazing source of complex carbs and fiber. The perfect way to kick start any day!
  6. There are limitless add-ins for these protein muffins! Before baking these healthy chocolate chip pumpkin muffins, you can add in shredded coconut, blueberries, strawberries, chocolate chips, or whatever your heart desires!
  7. Toddler and kid-friendly! Kids absolutely love these muffins, especially if you make them mini. They are the perfect size for kids and adults alike!

Happy Pumpkin Protein Muffin Bakin’!

Click to share with your friends & family!


  • Mykayla

    My one year old and three year old loved these muffins which is a win in my book since my three year old is so picky!

    • Claire

      I am so glad you made them and the picky eaters loved them! What a WIN!! Thanks for making them and sharing. Your support means so much! 🙂


  • April

    WOW!!! These pumpkin protein muffins are the best I’ve ever made! So fluffy and loaded with flavour! They were such a hit in my home that I had to make another batch right away!! Thank you for this recipe, a new fall favourite for me!!

    • Claire

      April, I am so glad you loved these muffins! Thank you so much for the sweet comment. Such a win when a healthy recipe is a hit. That’s my goal with all my recipes 🙂 I can’t wait to hear about what you bake next!


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