These low carb chocolate protein muffins are soft, fluffy and moist - almost like eating chocolate cake. They're made with almond flour, chocolate pea protein and pumpkin puree (no banana). In addition, these low sugar protein muffins are paleo friendly, flourless and dairy free.

Truthfully, protein muffins are my favorite type of muffin. But, believe it or not, this is the first chocolate protein muffin recipe I've put up on my site!
Now, I love anything chocolate. And I love muffins. So it's about time I sat down and created a chocolate protein powder muffin recipe. The results? Amazing!
These flourless protein muffins remind me of a moist cupcake. However, they're actually healthy, low in sugar and high in protein. You won't be disappointed! Unless, perhaps chocolate or muffins aren't your thing 😉
Why You'll Love these Chocolate Protein Muffins
- grain free and gluten free - these muffins are made without all-purpose flour, and instead use a combination of almond flour, pea protein, tapioca flour and cocoa powder
- paleo friendly - made with simple, wholesome ingredients
- dairy free - made without whey protein and without milk
- super moist - the addition of pumpkin puree makes these muffins super moist
- low carb - low in sugar and made without banana
- healthy but delicious - a must!

Ingredients
The full recipe for these low carb chocolate protein muffins can be found in the recipe card below, but here's an overview of the ingredients you'll need:
- blanched almond flour - these chocolate protein muffins are made with almond flour. If you need the recipe to be nut free, the best swap would be tigernut flour.
- chocolate protein powder - I recommend pea protein for this recipe. Pea protein is very absorbent, so if you're using another type of protein powder, you may have to use less almond milk.
- tapioca flour/starch - needed for the proper muffin texture. The best swap is arrowroot starch, but potato or cornstarch should work too.
- cocoa powder - for a chocolate muffin flavor. You can use cacao powder instead.
- baking soda - for a rise, resulting in a fluffy muffin.
- salt - enhances the flavors
- large eggs - needed to bind the ingredients. I don't recommend an egg substitute for this recipe.
- almond milk - to thin the batter. Any type of milk (or water) will work.
- pumpkin puree - adds moisture to the muffins, without much flavor.
- maple syrup - just a little to sweeten these chocolate protein muffins. You can use a liquid sugar-free sweetener instead if you want these muffins to be lower in carbs.
- vanilla extract - for flavor.

How to Make Chocolate Protein Muffins
These muffins are easy to make - here's how to do it:
- First, add all dry ingredients to a large mixing bowl. I recommend measuring the ingredients by weight (especially the almond flour and protein powder). I use a small food scale - it works extremely well and they are inexpensive.
- In a separate bowl, whisk together the wet ingredients.
- Pour the wet mixture into the dry mixture. Whisk the batter until it has a thick, even texture.

- Pour the batter into a lined muffin pan, filling each cup nearly to the top. Silicone muffin molds are a great alternative to paper liners! Because they are re-usable, they reduce waste and save you money. Plus, I rarely have an issue with baked goods sticking to them.

- Next, place the muffins in the oven and bake at 350 degrees F for 25 minutes. They come out fluffy, well risen and smell amazing!
- Lastly, remove the muffins from the oven, cool in the pan for 5 minutes, then transfer them to a wire cooling rack. When cooling them on the rack, I recommend removing them from the silicone muffin liners.

Storage
These muffins are best stored in the fridge in a sealed, air-tight container and eaten within one week.
More Low Carb Protein Muffin Recipes
Low Carb Chocolate Protein Muffins (No Banana)
- Prep Time: 10 minutes
- Cook Time: 25 minutes
- Total Time: 35 minutes
- Yield: 1 dozen muffins 1x
Description
Low carb, chocolate protein muffins - a great Paleo snack or grab-n-go breakfast. Kid friendly, low in sugar, moist and fluffy!
Ingredients
- 2 cups blanched almond flour (170g) sifted, spooned & leveled
- ½ cup Nuzest Rich Chocolate Protein (48g)*
- ¼ cup tapioca flour (32g)
- ¼ cup cocoa powder (20g) sifted, spooned & leveled
- ¾ tsp baking soda
- ¼ tsp salt
- 3 large eggs
- 1 cup almond milk
- ½ cup pumpkin puree
- 2 Tbsp maple syrup
- 1 tsp vanilla extract
Instructions
- Preheat oven to 350 degrees F.
- In a large mixing bowl, whisk together dry ingredients. This includes the almond flour, protein powder, tapioca flour, cocoa powder, baking soda and salt.
- In a separate mixing bowl, whisk together wet ingredients. This includes the eggs, pumpkin puree, almond milk, maple syrup and vanilla.
- Pour the wet mixture into the dry mixture and whisk until well combined.
- Pour batter into a lined muffin pan. Fill each slot nearly to the top, making 12 muffins.
- Place the pan in the oven and bake at 350 degrees for 25 minutes.
- Cool 5 minutes in the pan, then transfer the muffins to a wire cooling rack.
- Best stored in fridge up to one week.
Notes
For best results, I recommend measuring ingredients by weight when given.
These muffins are not super sweet. If you want them to be sweeter, I recommend adding in a couple tablespoons of granulated sugar (like coconut sugar or maple sugar).
*This recipe has only been tested using Nuzest pea protein powder, which is extremely absorbent. If you use another type/brand of protein powder you will likely need less almond milk. That being said, I cannot guarantee results if using a different protein.






Jen
Will this recipe work if I use a vegan protein powder? Also, is there anything I can substitute for the arrowroot?
Katie
Hi! The protein powder I use IS Vegan, so most other vegan protein powders should work. I would substituted by weight. You can use tapioca flour in place of the arrowroot.
Deborah
Hey will this work with oat flour ? What is the equivalent ?
Can you give the diameter and measurements of each muffin tin? Do you blend ingredients with an electric mixer or with a whisk ( which one? ) thanks in advance
Katie
Hi! I do not use oat flour in any of my recipes (not Paleo) so I don't have much experience baking with it. Not sure how well it works as a substitute for almond flour. These muffins are standard size, 2" diameter. I use a whisk to mix the batter.
Deborah
Thanks
Can i replace the 3 whole eggs by 6 egg whites? Any experience with pumpkin puree or apple sauce? Is it true you do not taste them in a chocolate cake? And that they can replace eggs?
Will it make any difference Whether i use water or nut milk? Thanks
Katie
I recommend keeping the eggs as-is. I have only tested these muffins with the ingredients given in the recipe. That being said, water or nut milk will work.
Deborah
Hello can I swap blanched almond flour for almond meal? In what quantities? Will adjustments need to be made? Thx
Deborah
Hey
When i weigh 1/4 cup of my cacao powder it is 15g not 25g and one cup of my almond flour weigh 90 grams so should i use cups or weigh the ingredients when making the recipe? Also can i use baking powder instead of baking soda here? When you make the recipe At home do you use water or nut milk?
Thanks
Katie
I would measure ingredients by weight - that's far more accurate. You could use baking powder, it shouldn't make a big difference. I would use 2 tsp baking powder in place of the 1 tsp baking soda. I use water when making these.
Deborah
Also do you fill cups 2/3 or 3/4 of the way up? Thx
Katie
Muffin cups are filled almost to the brim - the batter is thick. See blog post photos for an example. The recipe will make 12 muffins.
Kiara
Hi, is there any replacement for arrowroot flour? I have tapioca and coconut flour handy. Ty
Katie
tapioca works!
kerri
Hi, I had a question--I thought peas weren't paleo and was just wondering if something changed? I think I did hear peas were allowed on the Whole 30 now, so maybe on Paleo diet too?Thank you, they look delicious!
Katie
Hi! Peas are one of those "gray area" foods...some will say they're Paleo and some not. I consider them Paleo and include them in my diet from time to time because they tend to be easy to digest and don't cause GI stress like many other legumes.
Tina
Any idea on the nutrition content on these? TY!
Arlene
Hi
Can I replace the vegan protein with grass fed whey protein? I know it won’t be vegan any longer but that’s ok for me
Thank you
Katie
Hi! I don't think this recipe will work with whey protein.
Katie
This is one of my favorite protein muffin recipes! I love it and hope you all will too.
Ms ELAINE LOWE
Can you tell me the nutritional facts please?
Namely the amount of carbs? For the whole recipe?
Karla
Do you think it will work with collagen instead of the pea protein?
Katie
No, this recipe needs pea protein - it's super absorbent. Collagen will not work.
Jaye
Perfect muffins even when substituting the pea protein with whey. Light and fluffy and not too sweet.
Jennifer
Just made these this morning and OMG they are so good! I personally love that they aren’t too sweet, they are just right to me! Made some for my husband but had to add chocolate chips lol
Katie
I'm so glad you enjoyed them! I love that they aren't super sweet too 🙂
Liz
Do you think this would work with mashed cooked sweet potato instead of pumpkin for a bit more natural sweetness? Excited to try!
Katie
Yes, I think that swap would work well!
Melina
Hi! Can I swap pumpkin for banana? I have some seriously brown bananas!!!
Katie
That should work!
Sharon B.
First time making these and they’re really good and moist. I used a different brand of pea protein powder, substituted garbanzo flour for the tapioca flour and added 2 more tablespoons of maple syrup after tasting the batter. Also, I added a few chocolate chips to each. Baked them 22 min., and that worked. I added up the protein grams for all ingredients, and divided by 12, coming up with about 8 grams per cupcake, but your notes at the beginning say 20 grams per serving. Can you tell me how you got that? Thanks for the recipe, I will make these again.
Katie
I'm so glad you enjoyed the muffins 🙂 The 20g of protein per serving was referring to the pea protein I used, not the muffins.
Emma Westcott
Hello
I came here to thank you for the recipe. I've just eaten one of the muffins 2 days later and they're still moist and fudgey. I swapped pumpkin puree for sweet potato because that's what I had at home. I also through in a small handful of dark chocolate chips. Yummy!
Katie
Hi! I'm so glad you like them and that sweet potato worked just as well 🙂 Thank you for leaving a review!
wlwlanz
These look delicious but what’s the macro count for each muffin?
Katie
I'm not sure, but feel free to use an app like myfitnesspal to calculate it yourself.
Addisen McNally
Hi! I was wondering how many calories 1 muffin is?
Katie
Hi! I haven't calculated the calories or macros for these muffins, but you can do so in an app like MyFitnessPal.