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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46 thoughts on “Low Carb Pumpkin Protein Muffins”

  • I made these exactly as stated (I’ve been using Bowman Nutrition protein already, so I had the pumpkin spice on hand). I appreciated the ingredients listed by grams bc the recipe turned out perfectly. My entire family liked them! Next time I think I’m going to see if I can make a glaze. After being stored for a day, they were a little dry (but still delicious) and a glaze on top might help!

  • Loved these muffins! I substituted regular flour for almond flour at a 1:1 ratio and they came out perfect! Once I saw/tasted how great they were I made a second batch with chocolate chips on top!

  • I have many Bowmar Nutrition products, and I love experimenting with them and using the protien to make new creations. This is by far one of my favorite things that I have made using the protein! I love pumpkin bars so I added a cream cheese type frosting to mine.

  • I love these muffins. They taste great and were so easy to make. The taste of the muffins are a spicy pumpkin. I put them in the freezer and took them out as I needed them. Popped them in the microwave for a few seconds and they tasted like I just made them.

  • Really great recipe! I turned mine into donuts and substituted a different protein powder, added some pumpkin pie spice and they still turned out great. Mom and baby approved!

  • These are so simple to make and taste like I spent hours prepping! Subbed KC buttermilk for almond flour and they tasted perfect! They’re a new addition to my weekly meal prep 😬

  • These were delicious! I only had vanilla protein on hand so I subbed that and added in about a tesspoon of pumpkin pie spice to add to the flavor. They came out super moist!

  • Made these the other day and used almond flour in place of all purpose flour. They turned out pretty good but were a bit dense. When I figured the nutrition out they only had about 2 net carbs. Definitely going to try them again using your method with AP flour. (Sidenote: I tried to tag you in my post by my profile is private , so I’m guessing you aren’t notified. I keep giving you shout out though 😉 keep the recipes coming!)

  • Loved these. I tried them last night for the first time and I might be hooked. I love pumpkin spice (call me a basic white girl…doesn’t offend me), however I didn’t have the Bowmar Nutrition protein so I used vanilla and added a ton of pumpkin spice and a little but of extra pumpkin and tried to keep it the same consistency. They still turned out amazing! I topped each one with some protein icing (vanilla mixed with some water until it’s a glaze) and they were divine! I don’t know if I can justify buying a whole tub of protein for one recipe…so I’m glad I found a way to still get the pumpkin flavor!

  • This was awesome. I followed the recipe exactly for the muffins. I made a frosting using powdered swerve, Greek yogurt cream cheese, light butter, pumpkin spice. Oh…I didn’t have the pumpkin spice protein powder so I used protein frosted cookie and added pumpkin spice. SO GOOD

  • We loved these!! I ended up making more than the recipe called for. My husband and I each had some for breakfast one weekend and there were still plenty left over for me to eat for a quick breakfast throughout the week! Great flavor and healthy-can’t beat it!

  • I made these in a mini muffin tin and added a few chocolate chips. They are perfect to grab before or after a workout. They freeze well, too.

  • Made these tonight but Blueberry version. Swapped bowmar Punpkin for the Blueberry cheesecake and the canned pumpkin with a tap of applesauce and fresh blueberries. Favorite new protein muffin recipe hands down!

  • Made these and they are so dang good! Only thing is I think I cooked them for too long so just keep an eye on them if you want them more moist. Either way they were still great!

  • Hi Mason ,

    I’m fairly new to your site . Thanks for all of your hard work .
    I just made the low carb pumpkin muffins . They do not look anything like your photo . They just look lumpy and no shine on theta like a typical muffin . I followed the recipe exactly including the recommended Protein powder . Any advice for me ?

    Thanks !

    • The usual suspects are measurement errors (measuring cups vs weighing ingredients), over baking, using different equipment (muffin tin vs muffin molds), and ingredient differences (sounds like this wasn’t the issue). If they’re lumpy, I’d say they might be under mixed. Other than that, I’d be guessing at some of the other things.

  • I’ve made these several times! I used vanilla protein powder since I can buy it in bulk and doubled the pumpkin pie spice. I find them a bit too bland to eat plain so I top them with frosting – balance! 🙂 Thanks for the recipe

  • I made these with Atkins protein powder. Fresh out of the oven it was a little overpowering. My daughter loved them. But after being in the freezer, they were delicious, and I heated one up every morning for breakfast. Making more this morning for the coming week.

  • Made these amazing pumpkin muffins. I did change the protein by using a pumpkin cheesecake flavored protein I had and they came out amazing! Such a great snack for work when I don’t have time for a meal between patients. And they’re GF which is exactly what I need. If you want to make them more carby just add GF flour instead; so good as well.

  • 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

  • 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 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!

  • 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!

    • 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.

  • 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.

  • 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?

    • 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!

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