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!

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
Ingredients
- 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
Instructions
- 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.
- Mix the dry ingredients together in a large bowl.
- Gradually stir in the eggs, canned pumpkin, and vanilla extract. Stir until you have an evenly mixed batter.

- Spoon the batter into the muffin tin or molds, filling each mold about 3/4 full.

- Bake for 23-26 minutes or until the muffins are cooked through and the tops are golden brown.
- Transfer the muffins to a wire rack to cool and enjoy!
Notes
- 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.







This is my go to muffin recipe. I make these almost weekly. I use half regular and half almond flour. I have made the true recipe several times but I also switch it up by omitting the pumpkin spice and adding different fruits like blueberries, raspberries, apples, etc, or nuts (walnuts or pecans) and either white or chocolate or cinnamon chips. I also experiment with different protein flavors too. This is a truly versatile recipe, definitely in my top 5 favorites.
These are my go-to treat lately! I typically use vanilla protein but just recently started using 1st Phorm’s ‘PSL’ variety for added pumpkin flavor and it’s so tasty! I make them for the week and enjoy them warm or cold. Paired with some sugar- free maple syrup or ice cream for a dessert!
Thank you so much Mason for your recipes, they help a vegetarian gal like myself sneak in protein without relying on bland protein bars!
I love these muffins! Texture is amazing – they’re super moist! The taste is perfect, and they definitely don’t taste low carb. These are a staple in my meal prep.
These were great! I subbed AP flour for the almond flour, egg whites for the eggs, and used Optimum Nutrition whey protein instead and they still turned out great. I think I added way more pumpkin pie spice than what a normal person would find acceptable but hey, I like my muffins spicy haha
These are so yummy! A co-worker first shared these with me and I made them for my family. Everyone loves them!
This is my go to muffin recipe. I make these almost weekly. I use half regular and half almond flour. I have made the true recipe several times but I also switch it up by omitting the pumpkin spice and adding different fruits like blueberries, raspberries, apples, etc, or nuts (walnuts or pecans) and either white or chocolate or cinnamon chips. I also experiment with different protein flavors too. This is a truly versatile recipe, definitely in my top 5 favorites.
I have made these with vanilla protein powder and a pumpkin spice protein, both were good but I need to add a little more pumpkin spice to the vanilla one. I top these with a pumpkin butter from a local orchard and they are amazing.
I have made these with vanilla protein powder and a pumpkin spice protein, both were good but I need to add a little more pumpkin spice to the vanilla one. I top these with a pumpkin butter from a local orchard and they are amazing.
I would like to substitute almond flour for bob mills gf all
purpose flour and use a bone protein powder verses the one in the recipe? Any thoughts would be appreciated?
That’s a lot of change to make at once. You might start with just the protein first if possible. When you do swap the flour, I’d start with a 1:1 substitution. That’s just a guess, though. Sorry I can’t be of more help!
I followed this verbatim, and mine came out totally different. I cooked for 25 mins and they came out looking fine, but like pudding on the inside. I put them in for an extra 20 mins, no change – the tops are golden brown but the inside is still like pudding. The flavor is fine, but I have to eat these out of a muffin cup with a spoon. No fluff to these muffins!