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Low Carb Pumpkin Protein Muffins

If you’re in search of a low carb breakfast OR a sweet treat to increase your protein intake, these low carb pumpkin protein muffins will do the trick. Each pumpkin muffin has 11 grams of protein with just 5 grams of carbs, though you’d never know it. They’re light and fluffy with just the right amount of moisture.

And to top things off, you’ll only need 7 ingredients and a mixing bowl to make these low carb pumpkin muffins!

If you're in need of low carb breakfast or snack ideas, you'll love these pumpkin protein muffins. They're super easy to make and have just 3 net carbs each!

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What You’ll Need to Make These Low Carb Pumpkin Protein Muffins 

Like I mentioned above, there are only 6 ingredients on the list. I’ll quickly run through the primary ingredients and touch on any potential substitution questions.

Almond Flour

As one of two primary structural ingredients, the almond flour is tough to substitute for. You could try using other low carb flour options like coconut flour, but the coconut flavor may be hard to mask.

If you have an almond allergy or simply don’t have almond flour on hand, you could substitute with all purpose flour or maybe even something like the graham cracker crumbs I used in my pumpkin banana bread protein muffins recipe.

With these options, I’d start with a gram for gram substitution and add as needed. I’ve provided a couple photos of what the pumpkin protein muffins batter will look like before baking for comparison.

Protein Powder

Our second structural ingredient is protein powder. I used PEScience Select which is a blend of whey and casein protein. It’s a bit thicker than a whey-only protein so if you’re using another protein powder, you may need to adjust slightly. 

I originally developed this recipe with a pumpkin spice flavored whey concentrate and used an extra scoop of protein powder and half the canned pumpkin. 

You can get an idea of the batter’s consistency from the photos in the recipe card below. As long as you’re pretty close, your protein muffins should be just fine.

Wet Ingredients

Canned pumpkin and eggs—that’s all you need in this department. The only thing I could think of in terms of ingredient substitutions here is if you had an egg allergy or used a vegan protein powder and needed to ditch the eggs.

In that case, you could probably get away with using more canned pumpkin and maybe a bit of unsweetened apple sauce to make up for the 150-200 grams of egg in this recipe.

Final Notes for These Low Carb Pumpkin Protein Muffins

In the recipe notes below, I dropped a link to my Amazon product list where you’ll find silicone baking cups. I can’t recommend these things enough. Nothing sticks to them, meaning no macro goes wasted on the side of paper baking cups or in the muffin tin.

Okay, that’s about it! If you make these low carb pumpkin muffins, I’d love to see ’em. Snap a photo and tag me on Instagram @mason_woodruff or join my free Facebook group and share it with the Proton Party.

low carb pumpkin protein muffins

Low Carb Pumpkin Protein Muffins

Yield: 8 muffins
Prep Time: 10 minutes
Cook Time: 20 minutes
Total Time: 30 minutes

A simple recipe for pumpkin spice muffins with 5 grams of carbs and 11 grams of protein each. 


  • 3/4 C (84g) Almond Flour
  • 2 scoops (62g) PEScience Protein Powder, vanilla
  • 1/2 Tbsp Pumpkin Pie Spice
  • 1/2 tsp Baking Powder
  • 3 large Eggs
  • 1 C (240g) Canned Pumpkin
  • 1/2 Tbsp Vanilla Extract, optional


  1. Preheat an oven to 350F and spray 8 slots in a muffin tin with nonstick cooking spray or place 8 silicone muffin molds on a baking sheet. 
  2. Mix the dry ingredients together in a large bowl.
  3. Gradually stir in the eggs, canned pumpkin, and vanilla extract. Stir until you have an evenly mixed batter.  low carb pumpkin protein muffins ingredients mixed in a bowl before going in the muffin molds
  4. Spoon the batter into the muffin tin or molds, filling each mold about 3/4 full.  low carb pumpkin protein muffins batter in the muffin molds
  5. Bake for 23-26 minutes or until the muffins are cooked through and the tops are golden brown. 
  6. Transfer the muffins to a wire rack to cool and enjoy!


  • Each muffin has 2 Smart Points.
  • You can find the silicone baking cups I use on my Amazon tools and products list.
  • The original recipe with Bowmar Nutrition pumpkin spice protein used 3 scoops (84g) protein powder and 1/2 cup (120g) canned pumpkin.
Nutrition Information:
Yield: 8 muffins Serving Size: 1 muffin
Amount Per Serving: Calories: 135Total Fat: 8gCarbohydrates: 5gProtein: 11g

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More Healthy Recipes with Pumpkin 

MaryBeth Barnum

Thursday 15th of April 2021

Another one of our many favorites!!! We love to add some chocolate chips in for the perfect crunch and a little extra sweetness :)


Thursday 25th of February 2021

How much does each serving size weigh?

Mason Woodruff

Friday 26th of February 2021

Just one muffin. I'm not sure on the weight of each. Sorry!


Sunday 15th of November 2020

These looked really great but I think I did something wrong...I used everything exactly, except I substituted a different protein, very similar to PE Science. It was so thick and did not look anything like your picture. I had to add some almond milk and I still couldn't get it to the consistency you had. Not sure what I did wrong. Any ideas?

Mason Woodruff

Monday 16th of November 2020

I reckon it's the different protein powder. It's rare to have a total success when substituting that ingredient, unfortunately. You had the right idea adding the milk but sometimes that'll throw off the ratios of other ingredients. It's hard to say what the fix would be. Sorry this one gave you trouble!

Rebecca Arbery

Saturday 10th of October 2020

Made these this morning. Used AP flour as I didn't need the low carb. Found that the batter was too thick. Added an additional egg and one applesauce packet. So yielded 9 muffins due to the extra volume. Taste wise, they were good! Had a different texture than I was expecting, but not off-putting. In full disclosure, this was my first time baking with protein powder. They did fall quite a bit after I took them out of the oven.


Wednesday 7th of October 2020

These are just the best. Make them often, not just for fall!

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