These 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. 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 😉
Chocolate Protein Muffins
Here 's what you need to know about these low carb 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 cacao powder
- paleo friendly
- dairy free - made without whey protein and without milk
- sweetened with maple syrup - no banana
- super moist - the addition of pumpkin puree makes these muffins super moist
- low carb
- healthy but delicious - a must!
These easy muffins can be made from start to finish in less than 40 minutes. They are satisfying, yet healthy and can be enjoyed any time of day.
Eat them on your way out the door for breakfast, pop them in school lunches or dress them up with some coconut whipped cream for dessert. No matter how you choose to eat them, they're sure to be enjoyed!
Ingredients
These almond flour protein muffins are made with a combination of grain free flours, protein powder, eggs and a few other simple baking ingredients. Here's what you need for the recipe:
Grain Free Flours
The three necessary flours for this recipe include: almond flour, tapioca flour/starch and cacao powder (or cocoa powder). Together, these three ingredients create a fluffy, moist and airy muffin.
The only substitutions would be to replace the tapioca flour with arrowroot starch and the cacao powder with cocoa powder. Either (or both) of these substitutions shouldn't have much affect on the overall taste or texture of the muffins. Just be sure to measure by weight!
Protein Powder
My number one choice for protein powder is Nuzest. Their protein powder is:
- made from premium European Golden Peas
- contains 20 grams of protein per serving
- is low in fat, carbs and sugar
- vegan and plant based
- free of all common allergens
- easy to digest
I see this protein as the perfect paleo protein powder because it is grain free, low in sugar and doesn't contain any fillers. Plus, it's easy to digest, works well for baking and I love the flavor.
For this recipe, I used the Nuzest Rich Chocolate. However, any Nuzest flavor will work. (My favorite flavor is the Smooth Vanilla.)
Eggs
Eggs are necessary! I love creating vegan recipes, but egg substitutes will not work well for these protein muffins.
Sweetener
Although sweetener isn't required, I suggest adding a little bit to give these muffins more flavor. I used maple syrup - a great paleo friendly option.
If you want a lower-carb option, then swap the maple syrup for any sugar-free liquid sweetener.
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 amazing! 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.
How To Store Chocolate Protein Muffins
These muffins are best stored in the fridge in a sealed, air-tight container and eaten within one week.
More Paleo Protein Muffin Recipes
Like I mentioned earlier, protein muffins are my favorite! And, I have a whole bunch of various low carb Paleo muffin recipes on my site. Here are some favorites:
PrintChocolate Protein Muffins (Low Carb, Paleo)
- 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 cacao 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, cacao 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.
Keywords: muffins, high protein, Paleo, chocolate, low sugar, snack, chocolate protein powder muffins, nuzest protein, pea protein muffins, low carb snack recipes, paleo muffins
Jen says
Will this recipe work if I use a vegan protein powder? Also, is there anything I can substitute for the arrowroot?
Katie says
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 says
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 says
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 says
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 says
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 says
Hello can I swap blanched almond flour for almond meal? In what quantities? Will adjustments need to be made? Thx
Deborah says
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 says
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 says
Also do you fill cups 2/3 or 3/4 of the way up? Thx
Katie says
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 says
Hi, is there any replacement for arrowroot flour? I have tapioca and coconut flour handy. Ty
Katie says
tapioca works!
kerri says
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 says
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 says
Any idea on the nutrition content on these? TY!
Arlene says
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 says
Hi! I don't think this recipe will work with whey protein.
Katie says
This is one of my favorite protein muffin recipes! I love it and hope you all will too.
★★★★★
Ms ELAINE LOWE says
Can you tell me the nutritional facts please?
Namely the amount of carbs? For the whole recipe?
Karla says
Do you think it will work with collagen instead of the pea protein?
Katie says
No, this recipe needs pea protein - it's super absorbent. Collagen will not work.
Jaye says
Perfect muffins even when substituting the pea protein with whey. Light and fluffy and not too sweet.
★★★★★
Jennifer says
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 says
I'm so glad you enjoyed them! I love that they aren't super sweet too 🙂
Liz says
Do you think this would work with mashed cooked sweet potato instead of pumpkin for a bit more natural sweetness? Excited to try!
Katie says
Yes, I think that swap would work well!
Melina says
Hi! Can I swap pumpkin for banana? I have some seriously brown bananas!!!
Katie says
That should work!