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.







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!
I’d double check your ingredient amounts or oven temperature. No way should these take 45 minutes and still be pudding like on the inside!
My husband bought almond flour meal instead of just almond flour. Can I use it for the above recipe?
I used blanched almond flour (without the skins) so using meal (with the skin) might make a slight texture difference.
I’m gong to try these but we are alergic to whey, do you think a protien powder without whey would work just as well?
It’s hard to say. They’re all a bit different. It may take a bit of trial and error to get the ratio right.
I made these using mashed banana instead of pumpkin and they turned out perfect. I’ll be using this recipe as a base for many different flavors in the future. Thank you!
I made these using mashed banana instead of pumpkin and they turned out perfect. I’ll be using this recipe as a base for many different flavors in the future. Thank you!
If I could give 10 stars I would for this recipe! I made these with my daughter as she was wanting a muffin to take to school in the morning for her mid morning breakfast. They were incredibly easy to make and tasted delicious. I added a few spoonfuls of unsweetened apple sauce to make my mixture a little less dense and instead of vanilla extract I used almond extract as I also added crushed almonds to the top to give the muffin a bit of crunch. They were phenomenal and my daughter’s friends were asking for the recipe so their mom’s could make them as well!
If I could give 10 stars I would for this recipe! I made these with my daughter as she was wanting a muffin to take to school in the morning for her mid morning breakfast. They were incredibly easy to make and tasted delicious. I added a few spoonfuls of unsweetened apple sauce to make my mixture a little less dense and instead of vanilla extract I used almond extract as I also added crushed almonds to the top to give the muffin a bit of crunch. They were phenomenal and my daughter’s friends were asking for the recipe so their mom’s could make them as well!
Like!! Really appreciate you sharing this blog post.Really thank you! Keep writing.
I can’t eat whey, can I just omit the protein whey or do I need to substitute with something? Thanks in advance
You might be able to substitute the protein powder for more almond flour. Though you’ll probably need quite a bit to make up the difference. I wouldn’t omit without reducing the amount of pumpkin.
Could you use coconut flour instead of almond flour?
I wouldn’t recommend it. They’re quite different and would require some tinkering to figure out the right ratio.