
Start your day off right with these easy protein muffins. Packed with fiber, healthy fats, and 12g of protein per serving. And plenty of chocolatey goodness too!

If you follow me regularly, you know I have a deep and abiding love for keto muffins. I love creating the recipes and I love eating the results!
And these chocolate protein muffins are easily among my new favorites. They are fluffy and moist, with a rich chocolate flavor. And the added protein gives me the boost I need to tackle a tough workout or a long run.
It’s a healthy keto breakfast or snack that tastes like a cupcake. How can you say no to that?

Why you need to try them
These muffins are perfect for people looking to get more protein into their keto diet. The keto diet has evolved over the past few years and it’s no longer ALL about the fat. And it’s not a one-size-fits-all approach.
Many people, especially women, find they do better with a little less fat and a little more protein. As we age, our bodies process protein less efficiently, so we need more of it to maintain muscle mass.
But sometimes a high protein meal like meat feels like too much work or just too heavy. So protein snacks that are easy to grab can fill that void. You can make a big batch of these keto protein muffins and sock them in the fridge or freezer.
They have 12g of protein per muffin, only 1.6g net carbs, and no added sugar. Oh and did I mention that they’re fudgy and delicious? That certainly doesn’t hurt either!

Ingredients you need:
- Nut butter: I used pecan butter for this recipe but you can really use any nut or seed butter you like best.
- Sweetener: I like Swerve Brown for these protein muffins, as it deepens the flavor. But they don’t rely on a specific sweetener for consistency so you should be able to use your favorite. Do keep in mind that allulose may make them extra soft.
- Chocolate collagen protein: You can’t have protein muffins without protein! I found that collagen protein worked best for consistency and also provides a better protein content. Whey protein works as well but they tend to be more dry. See the expert tips section for more information.
- Cocoa powder: Dutched cocoa powder gives these muffins a rich, deep chocolate flavor.
- Sugar free chocolate chips: I used the dark chocolate chips from ChocZero.
- Kitchen staples: Vanilla, eggs, baking powder, salt
Step by Step Directions

1. Combine the wet ingredients: Place the nut butter in a large bowl and stir well to mix in the oils. Whisk in the sweetener and vanilla extract until well combined, then whisk in the eggs until smooth.
2. Add the dry ingredients: Add the collagen, cocoa powder, baking powder, and salt and stir until well combined. Stir in the chocolate chips.
3. Bake the muffins: Divide the mixture evenly among parchment or silicone-lined muffin cups. Bake in a 350ºF oven for 18 to 25 minutes, or until the muffins have risen and are just firm to the touch on top.

Expert Tips
I used pecan butter for this recipe only because I had some to use up. But really any nut or seed butter will work in these protein muffins. Consider almond butter, sunflower seed butter, or even peanut butter (yum!). The carb count may change somewhat depending on what you use.
I highly recommend collagen protein powder (aka collagen peptides) for these muffins. It combines really well with the nut butter and makes them both moist and fluffy.
I’ve tried whey protein but it’s not quite the same and they dry out more easily. If you do decide to go with another kind of protein, you may need to add a little liquid to thin out the batter and make it scoopable. 2 to 4 tablespoons of water or coffee should suffice. Make sure to remove them from the oven the moment they seem firm to the touch so that you don’t over bake them!
Frequently Asked Questions
Protein powder is actually very useful in keto baking, as it helps the consistency of many cakes and muffin recipes. It mimics the protein in gluten, so the baked goods rise better and become more fluffy. Check out my Keto Cake Recipes to see how it works.
Conventional chocolate muffins can have upwards of 30g of carbs per serving. Yikes, that’s a blood sugar spike waiting to happen. However, these Chocolate Protein Muffins have 5.2g of carbs and 3.6g of fiber, so they have only 1.6g net carbs per serving.
Animal protein such as fish, meat, poultry, and eggs is the most bio-available source of protein for the keto diet. So that should be the focus of much of your meals. However, easy snacks that contain added protein can help too. These protein muffins make a fabulous grab-and-go breakfast or snack.


Chocolate Protein Muffin Recipe
Equipment
Ingredients
- 1 cup (256 g) pecan butter, (or any nut/seed butter)
- 1/2 cup (91 g) Swerve Brown
- 1 tsp vanilla extract
- 3 large eggs
- 1/2 cup (54 g) chocolate collagen protein
- 3 tbsp cocoa powder
- 2 tsp baking powder
- 1/4 tsp (0.25 tsp) salt
- 1/3 cup (60 g) dark chocolate chips, sugar-free
Instructions
- Preheat the oven to 350°F and line a muffin pan with 12 silicone or parchment paper liners.
- Place the nut butter in a large bowl and stir well to mix in the oils. If it is very stiff, you can microwave it or heat it gently in a pan until it is more liquid.
- Whisk in the sweetener and vanilla extract until well combined, then whisk in the eggs until smooth.
- Add the collagen, cocoa powder, baking powder, and salt and stir until well combined. Stir in the chocolate chips.
- Divide the mixture evenly among the prepared muffin cups and bake 18 to 25 minutes, or until the muffins have risen and are just firm to the touch on top.
- Remove and let cool in the pan.
Video
Notes
Nutrition
Nutritional Disclaimer
Please note that I am not a medical or nutritional professional. I am simply recounting and sharing my own experiences on this blog. Nothing I express here should be taken as medical advice and you should consult with your doctor before starting any diet or exercise program. I provide nutritional information for my recipes simply as a courtesy to my readers. It is calculated using MacGourmet software and I remove erythritol from the final carb count and net carb count, as it does not affect my own blood glucose levels. I do my best to be as accurate as possible but you should independently calculate nutritional information on your own before relying on them. I expressly disclaim any and all liability of any kind with respect to any act or omission wholly or in part in reliance on anything contained in this website.
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Thank you for this amazing recipe! I have made them 4 times in the last 6 weeks. Yummy and healthy!!
I already have unflavored collagen peptides would that work or should I purchase the chocolate to get a more chocolate experience? I am a chocolate addict!
BTW – I have been using your recipes since I started Keto in 2020. I have enjoyed all your recipes – You are my hero – I wouldn’t have been so successful without these recipes! Thank you
Use the one you have and add 1 tbsp more cocoa and 1 tbsp more sweetener. You may need to add more liquid, as more cocoa will make the batter a little thicker.
I can’t wait to try this recipe!
The only kosher collagen peptides I’ve been able to find are unflavored.
Do you have any suggestions as to how to adapt the recipe to this? How much additional cocoa powder would you recommend adding? Would you make any other changes?
Thank you so much for all you do!
Yes, add another tablespoon of cocoa powder and a bit more sweetener.
These are amazing! I’ve made at least half a dozen batches (so far). These also freeze beautifully & they are also travel-friendly. I’m always looking for high protein breakfast & pre/post workout snacks: this one is already a ‘staple’ in my diet. 🙂
We were absolutely blown away at how amazing these tasted! Better than any full sugar or full grain muffin we’ve ever had! I used Costco almond butter and Cookies and Cream Mountain Ops Whey Protein, so I added 1-2 T avocado oil and 4T coffee. They were incredibly moist and delicious without being overly sweet. Just perfect. New recipe on the weekly rotation!
These chocolate protein muffins are so good – a real treat. I make them often so I always have some in the freezer.
just made these and ate one, yum!! I used almond butter and it was the thickest batter I’ve ever seen, worried it wouldn’t bake, but it did! love how low carb and high protein this is for pregnancy cravings. I used whey protein, didn’t let them cool in the pan too long.
I had my eye on this one for a long time and even bought some chocolate collagen powder for it. I don’t know why I waited so long; they are delicious! So delicious that I cheated and had a second one right away.
I used almond butter, and the batter was very sticky but workable.
I used the maximum cooking time, and I think that next time I’ll shorten the cooking time a bit, as they were just on the edge of dry. I think cooking them less will make them more fudgy.
Thanks for this great recipe. It will make a nice alternative for my breakfast. I was getting sick of bacon and eggs.
I read your blog but still wondering if Equip chocolate protein powder could be used in place of the collagen.
I got my question answered by reading the older comments. Am good to go now!
I rated these a 5 on looks alone! Haven’t tried the recipe yet. I’d love the link for your silicone muffin cups. The ones I have are not very good – all muffins stick no matter how I prep the cups or how long I let them cool before removing. I do wait like you have said.
These are SO fudgy and moist! I did get an annoying “chemical” taste that I think might be from the cheap silicone liners I used. (They smell nasty!) I tried to find the ones that you recommend, but they’re out of stock! Any suggestions for a replacement?
First time to bake these muffins, I used peanut butter and did add the 1/4 water. I didn’t have the chocolate collagen protein so I increased the cocoa to 4 T. I used collagen peptides that I already had. I will make these again . I’ve ordered the chocolate collagen protein for next time .
So moist and chocolatey!! Even non-keto family members go crazy for them!!
Can’t make them fast enough! Whole family loves them!
First, these muffins came out perfect! I used almond butter, and unflavored collagen protein powder. I added an extra tablespoon of cocoa powder and sweetner. I have a professional oven so I baked them for 15 minutes, which worked well for my oven. As with all keto baking, you have to monitor the baking time closely . They are tasty, fluffy, and chocolatey. What more could you want?
Thank you for sharing what you used as a sub for the chocolate collagen powder! I only have unsweetened collagen powder but really want to make these. Good to know 1 Tbsp extra cocoa and sweetener do the trick. I’m going to make these right now!
How much maple syrup do you suggest if i don’t have the sweetener you recommended
Sorry, I can’t really help. I don’t use maple syrup and it introduces more liquid to the recipe. Seems like you will need to experiment.