Pumpkin Protein Muffin

Tender pumpkin protein muffin recipe made with fresh pumpkin pulp, warm fall spices and extra protein. Serve these healthy pumpkin muffins for a quick breakfast on the go or enjoy for an afternoon snack.

Two pumpkin protein muffins on top of the other in black and white checkered muffin liner.

Pumpkin Protein Muffin

It’s time, friends! Pumpkin season is officially here and this time I’m ready to start the season with healthy pumpkin protein muffins!

I’m not sure if this is true, but on social media it has been rumored that there is a pumpkin shortage.

That threw me in a panic because the season is just starting! I also read that Trader Joe’s had plenty of pumpkin, so not to fret.

The only thing I can think about the initial panic is that maybe shipments are delayed in some parts of the country.

Luckily, I live very close to Trader Joe’s store so I popped over right away. Guess what? There were plenty of cans of pumpkin!

Although, I will admit that when I saw those full shelves, I immediately felt the need to hoard a dozen cans. Crazy thinking!

My senses came back and I deferred, and I left plenty of pumpkin for you to make these pumpkin protein muffins too!

Two cans made it home with me as well as two real baking pumpkins to make my own pumpkin puree.

All is good.

Fresh pumpkin puree in a glass jar.

Baking With Protein Powder

In this recipe I add an extra boost of protein using Greek yogurt and protein powder.

I use the same protein powder I make my smoothie drinks with. I like unflavored or vanilla whey low calorie and low carb protein powders.

Although I have also experimented with soy and pea proteins and the results were similar.

The key to baking with protein powders is to bake at a lower temperature. Otherwise, the muffin won’t hold in the moisture and will be dry.

Lower the baking temperature 325°F as noted in the recipe card. Resist the temptation to raise the temperature to 350°F when baking these muffins.

If you tried my zucchini protein muffins, then you will know why I decided to expand my flavor options to include a tasty pumpkin protein muffin.

Tender and flavorful and won’t send your glucose levels spinning out of control.

Top view of pumpkin protein muffin with cream cheese on the side.

Sugar Free Muffins

These aren’t too sweet and the extra boost of protein sticks to the ribs so you won’t be hungry immediately after eating!

This is another recipe I chose to not bake with granulated sugar.

I have found that once you limit your sugar intake, the cravings for sweets diminish greatly and overly sweet treats aren’t as appealing.

However, if you are easing into a low carb or sugar free diet, then adjust the sweetener in the batter to suite your preference.

Another delicious option is to drizzle the pumpkin protein muffins with a basic sugar glaze with Lakanto Powdered Monkfruit Sweetener (affiliate).

A top view of pumpkin protein muffin sliced in half.

How To Bake Pumpkin Protein Muffins

This recipe is just as simple to bake. We will whisk together the dry ingredients, then separately mix the wet ingredients before combining the two together.

  1. Combine the dry ingredients in a large mixing bowl.
  2. Separately mix the wet ingredients.
  3. Combine the wet and dry ingredients together.
  4. Place batter in muffin liners and bake at 325°F for 15-20 minutes.

Frequently Asked Questions

I Don’t Like Coconut Oil. What Can I Use Instead?

If you do not like the flavor of coconut oil, then look for coconut that is refined. Refined coconut oil is neutral tasting and doesn’t have the coconut smell.

On the other hand, any neutral tasting oil will work in this recipe. Use your favorite type, but I would stick with a healthy oil option like canola or avocado oil.

Baked pumpkin protein muffins in a baking pan.

How Much Protein Is In Each Muffin?

This will vary depending on the brand of protein you use. The type I use has 30 grams per serving.

In addition, the Greek yogurt and eggs also adds additional protein.

In order to know the exact macronutrients, add each ingredient in a recipe analyzer like My Fitness Pal or Verywellfit.

Below are the macronutrients from Verywellfit recipe analyzer.

Macronutrient nutrition label for pumpkin protein muffins.

Are These Muffins Keto?

No. Although, these muffins are made with healthy ingredients, this recipe is not keto due to the whole wheat flour used.

If you are not sensitive to some flour, these muffins may still fit in your macronutrients.

Once divided, each muffin will use about a tablespoon of whole wheat flour.

How Many Carbs Are In Each Muffin?

These muffins without add-ins net 10.8 carbohydrates. In comparison, traditional pumpkin muffins will be 30 carbohydrates or more.

How Do I Know My Pumpkin Is 100% Pumpkin Pulp?

The only way you can determine if the pumpkin puree you add to your pumpkin protein muffins is if your make your own pumpkin pulp.

Although many brands state 100% pumpkin on the label, the USDA allows for several different types of squash to fall in that category.

I explained this in this pressure cooker pumpkin puree recipe.

For that reason, I prefer to make my own pumpkin pulp so that I know when I use it, it’s 100% pumpkin.

Half of a pumpkin muffin topped with cinnamon cream cheese.

What Other Ingredients Taste Good With Pumpkin Protein Muffins?

The flavor options are endless! Here are some delicious ideas to add to your muffins to change up the flavor profile.

  • Chocolate chips – add 1/3 cup of baking chips (sugar free is my preference) to the batter. Save a couple to add to the top of the muffin the last five minutes of baking.
  • Nuts – Fold or sprinkle on top 1/2 cup of chopped walnuts, pecans, almonds or pumpkin seeds.
  • Coconut flakes – fold in 1/3 cup of coconut unsweetened coconut flakes.
  • Dried Fruit – fold in 1/3 cup of dried fruit like cranberries, cherries or blueberries.
  • Sugar glaze – drizzle a confectioner’s glaze on top similar in this strawberry bread recipe.
  • Top with Pumpkin Spice Butter Spread (pictured) – delicious way to add some extra flavor.

See, there are so many more options! Let me know how you make these protein pumpkin muffins uniquely yours.

Horizontal view of a half dozen baked pumpkin muffins on a cooling rack.

How Long Will Pumpkin Muffins Last?

If you cover your muffins in an airtight container these muffins will last for 5-7 days in the refrigerator.

These pumpkin muffins can be frozen for up to 3 months.

To freeze, cool the muffins completely. Wrap each muffin with freezer wrap and place in a ziplock freezer bag. Label with a “use by” date.

When you are ready to enjoy, place in the refrigerator overnight to defrost.

Alternatively, you can place frozen muffin in the microwave and turn on the defrost mode before enjoying.

You also might like this Savory Keto Muffin. Check it out!

Two pumpkin protein muffins on top of the other in black and white checkered muffin liner.

Pumpkin Protein Muffins

Pumpkin protein muffins with real pumpkin puree and fall spices. The extra protein in these are the perfect amount to provide a healthy muffin for breakfast or snack.
4.78 from 9 votes
Print Pin Rate
Course: Baking
Cuisine: American
Prep Time: 10 minutes
Cook Time: 15 minutes
Total Time: 25 minutes
Servings: 12 muffins
Calories: 219kcal
Author: Sandra Sandra


  • 1 cup whole wheat pastry flour
  • 1/2 cup whey protein powder plain
  • 2 teaspoons pumpkin pie spice
  • 1/3 cup golden monkfruit granulated
  • 1/8 teaspoon kosher salt
  • 1 teaspoon baking powder
  • 1 cup pumpkin puree
  • 1/3 cup coconut oil melted and cooled
  • 1/4 cup plus 2 tablespoons, Greek yogurt, plain
  • 2 egg
  • 2 teaspoons vanilla extract


  • Lightly grease muffin liners or muffin tin with cooking spray.
  • In a large mixing bowl whisk together flour, protein powder, pumpkin pie spice, sweetener, salt and baking powder.
  • In a separate bowl mix the pumpkin puree, coconut oil, eggs, yogurt and vanilla extract together until well combined.
  • Form a well in the middle to the dry mixture and pour the wet mixture in the center.
  • Fold all ingredients together with a rubber spatula. Don’t over mix.
  • Add 1/4-1/3 cup to each prepared muffin liner.
  • Bake at 325°F for 15-20 minutes or until a toothpick comes clean when placed in the center of the muffin.
  • Remove from oven and let sit for 5 minutes before transferring the muffins to a cooling rack.


Serving: 1g | Calories: 219kcal


Please note that the nutritional information provided are guidelines and may vary based on the brand of products used. For your specific nutritional goals use My Fitness Pal or Verywell Fit recipe calculators. All content within this site is not intended as medical diagnosis or treatment and should not be considered a substitute for professional medical expertise.


Healthy pumpkin muffins with an extra dose of protein that sticks to your ribs. These sugar free muffins make a great breakfast, snack or afternoon snack!
Hugs Sandra Signature

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    1. These are very good. I just made them but I calculated the macros and I am getting about a fourth of the total protein. Wondering how you got so much protein calculated for these.

      1. Hi Alison, I’m so glad you liked the recipe. The protein will vary depending on the brands you use. I’ve found the analyzers vary too. Now I’m going to have to make again and see what I come up with!

  1. A perfect treat to start the day off with. I love finding new ways to add protein into my diet. I esp love adding protein powder to my baked goods. These look so good!

  2. I’m always looking for new ways to add protein to my diet and these are definitely going to be a part of the meal plan. Thanks for another hit recipe!

  3. Yummy, healthy Muffins! I love how pumpkin melds with warm spices giving perfect fall delicacies and this is one of it! I have made fresh puree couple of days back, I know what I have to make with it now, thanks for sharing! 🙂

    1. This looks sooo good!! What can I sub for monk fruit?? I don’t have access to that and have never used it.

      1. Hi Caitlyn! You can use any sweetener of your choice. Monk fruit is a substitution for granulated sugar, and the replacement is 1 to 1. Other substitutions may be different, so it’s best to read what the package recommends.

  4. Breakfast. Definitely breakfast. I love all things pumpkin and spiced, these are definitely going to be the way I start the day! I love that they have the extra protein in them – perfect for the days I go kickboxing.

  5. It always blows my mind that canned pumpkin filling isn’t always pumpkin. I like to make my own too that way I know. These muffins are such a great way to make use of homemade puree.

  6. I have been looking for JUST this kind of recipe! A yummy muffin with protein and sweetener, and LOVE pumpkin. Thanks for the recipe!