Healthy Pumpkin Protein Muffins

These fluffy and soft Pumpkin Protein Muffins are a delicious fall breakfast or snack on-the-go. Packed with 8 grams of protein from whole wheat flour, Greek yogurt and vanilla protein powder. Plus, all the pumpkin flavor!

two muffins stacked on top of each other on a baking rack

I love baked goods during the cooler months. Hello, banana bread and ginger snap cookies!

We have a pumpkin bread recipe we make on repeat in the fall, so I decided to create a pumpkin muffin recipe to change it up! These muffins are not only full of pumpkin flavor but also pack a nutritional punch.

They're high in protein, making them a great grab on-the-go snack or complete a healthy fall-themed breakfast!


Okay, now time for the fun part - baking! The best part is how quickly and easily these muffins come together!

collage of making the pumpkin protein batter for the muffin tins
  1. Start by getting your dry and wet ingredients mixed well in separate bowls.
  2. Form a well in the dry ingredient bowl and pour the wet ingredients into it. Fold the ingredients together until you get your pumpkin muffin batter! Do your best to not overmix the batter. Otherwise, the muffins will be tough!
  3. Scoop into the muffin tins all the way full and bake for 25-30 minutes at 350 degrees Farenheight.
  4. The hardest part is letting them cool, but you definitely want to so that the center of the muffin sets - they're so soft!

Serving Suggestions

If having these muffins as breakfast, try paring them with cottage cheese, yogurt or fruit.

I LOVE Trader Joe's Pumpkin Butter. Oh my it's just one of those things I wait for to be fact I went to Trader Joe's on the first day of fall just to snag one of these guys! So worth it! Pumpkin butter on these healthy pumpkin muffins is just divine - an absolute must-try!

Recipe Tips and FAQs

What type of protein powder can I use?

I personally use a pea protein powder since it's high in iron, but you can use whatever you prefer!

How can I get my muffins to rise for maximum fluffiness?

Important question! Here's the key: don't let the batter sit. Once you mix the wet into the dry ingredients, quickly get the muffins in the oven. This allows the baking soda to do its best magic aka muffin fluffin' time!

Can you freeze the muffins?

Yes, absolutely! I love to make a bunch at once and pull them out of the freezer as I go through them. They heat up well in the microwave.

What can I do with the leftover pumpkin puree?

You can refrigerate it or freeze it to use later. Freezing it in dollops is great when you want to add just a little to a sauce or smoothie. You can also check out my recipes Pumpkin Bisquick Pancakes and Pumpkin Spice Kefir Smoothie for more fall foodie inspo!

bite taken out of a muffin resting face up on top of other muffins
two muffins stacked on top of each other on a baking rack

Pumpkin Protein Muffins

When you need a snack to grab on the go or an easy breakfast, these pumpkin muffins are a great option! Full of plant-based protein and spiced fall flavor!
4.34 from 3 votes
Print Pin Rate
Prep Time: 10 minutes
Cook Time: 20 minutes
Total Time: 30 minutes
Servings: 9 muffins


  • 1.5 cups whole wheat flour
  • ½ cup vanilla protein powder
  • 1.5 tablespoon pumpkin pie spice
  • ½ teaspoon baking soda
  • ½ teaspoon salt
  • 15oz canned pumpkin
  • ½ cup milk
  • ½ cup Greek yogurt
  • ¼ cup avocado oil
  • ½ cup honey
  • 1 teaspoon vanilla extract


  • Preheat the oven to 350 degrees Fahrenheit.
  • Add the dry ingredients in a bowl: whole wheat four, protein powder, pumpkin pie spice, baking soda and salt and mix well. In a separate add the remaining wet ingredients: milk, canned pumpkin, Greek yogurt, avocado oil, honey and vanilla extract and mix well.
  • Create a well in the dry ingredients to pour the wet mixture into and mix together with a whisk or spoon being careful to not over mix. Overmixing will cause tough muffins.
  • Fill 9 muffin tins all the way full and bake for 20-23 minutes or until a knife comes out clean.


  1. Try to get the batter in the muffin tins as soon as possible once the batter is mixed to allow the baking soda to do its best work in leavening the muffins.
  2. You can use any protein powder you prefer. I use a pea protein powder. If you don't like the chalky taste of most protein powders, try a collagen powder since they tend to have no flavor.
  3. Eat within a week if refrigerating. Otherwise, freeze them for up to 3 months. They reheat well!
  4. You don't have to follow the instruction for making 9 muffins. You can definitely break the batter up into a dozen muffins, but to get 8g of protein per muffin, you'll need to pour the batter for 9 muffins exactly. So, if protein matters to you then go for 9; otherwise, don't worry about it! 


Calories: 222kcal | Carbohydrates: 33g | Protein: 8g | Fat: 7g | Saturated Fat: 1g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 4g | Cholesterol: 14mg | Sodium: 218mg | Potassium: 137mg | Fiber: 2g | Sugar: 17g | Vitamin A: 297IU | Vitamin C: 1mg | Calcium: 77mg | Iron: 1mg

(Nutrition values are calculated by third-party software and an estimate that can vary based on product brands and cooking methods.)

Course: Breakfast, Snack
Cuisine: American
Keyword: pumpkin protein muffins, healthy pumpkin muffins, whole wheat pumpkin muffins, pumpkin muffins with yogurt
Tried this recipe? I love seeing your creations!Mention @monicanedeff.rdn or tag #monicanedeff so I can share them with the community!

13 thoughts on “Healthy Pumpkin Protein Muffins”

  1. Would love to try these! What would you recommend for substitute for the honey? Can I use brown sugar? Equal amounts?

    1. Hi Jan! Since brown sugar isn't a liquid it might change the texture. I would recommend using maple syrup instead!

      1. Thank you for such a quick response! I will be post transplant and I know honey is not recommended. I can't find info on the maple syrup but thinking it may be like honey. If I use brown sugar, maybe I can increase one of the liquids by a little? I appreciate any suggestions? I'm excited to try these for the high protein!

        1. Oh, I completely understand! Maybe try heating the brown sugar in some water in a saucepan until you get the consistency of honey, and then substitute it at a 1:1 ratio. I think that would be your best bet with trying to judge how much water to add. I hope this helps and wishing you a fast recovery!

  2. 4 stars
    Nice taste. Added some mini chocolate chips to entice the tiny humans! Took waaaaay longer than expected cook time. Closer to 45 and still kind of gooey so not sure if I messed up somewhere. Will try again and see how it goes

    1. Hi Isabel! Glad you and your family enjoyed them! That is interesting they took close to 45mins to bake. Did you substitute any ingredients?

      1. Only coconut oil for avocado oil and oat milk for regular milk. Going to try them again tonight and see what happens. The kiddos really loved them so still calling it a win!

    1. Hi Michele! Thanks for your rating and comment – so glad you enjoyed them! Yes, the nutritional information is for 1 of the 9 muffins.

  3. 4 stars
    Good texture and I like the addition of yogurt and protein. I also like the amount of pumpkin. I made mini muffins for my toddler. My husband said they weren't sweet enough, but he's comparing to fattening sugar filled muffins from a bakery. I'm happy with this recipe.

    1. Yeah, these are more "healthy" muffins, so not as sweet as typical bakery ones! Glad to hear you all enjoyed them, thank you for sharing!

Leave a Comment

Your email address will not be published.

Recipe Rating

Scroll to Top