
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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I haven’t made these yet but am dying to. Can I use Orgain Vegan Pea Protein in these?
I have several containers of it in the pantry and wish to use them up.
So using another protein powder, rather than collagen, can work but… they can dry out much more easily. I would reduce it to about 1/3 cup, and then watch them in the oven. Once that top is firm to the touch, get them out immediately.
These are wonderful. As soon as I tasted the first bite, I wished I had doubled the recipe! You are the queen of keto desserts. I’ve lost count of the number of people to whom I’ve recommended your recipes.
Do you think I could use whey protein? I don’t have collagen protein
Whey protein causes these to dry out a lot more. You can try it but take them out a bit early… check on them often and when they’ve risen fully, get them out of the oven.
I’m addicted to these! They are easy to make and relatively nutritious while satisfying my sweet tooth. Thank you for sharing 🙂
perfect and delicious. picture worthy
Carolyn: You have literally saved my life with all of your wonderful, tasty, easy recipes! I’ve been T2 diabetic since about 2006, undiagnosed until 2011. I tried keto before really understanding it, and was never really totally keto. My BG has remained around 240 all that time (WITH medication) as I was fudging on eating healthy keto foods and cheating. Until now. With your huge recipe collections, I am making progress to reduce my BG levels. The easy breakfasts, and especially snacks that allow me to have a treat that is GOOD for me is unbelievable. I’m now totally into ONLY keto foods. I have 3 of your cookbooks, another on the way and daily get emails for more great recipes. THANK YOU.
You need to know how much you have changed my life since becoming diabetic from stress at work.
May God bless you and your life.
Fabulous to hear!
I have only unflavored collagen. Suggestions?
This is a great recipe! I highly recommend making it. I used almond butter and it works well.
I make mine with sugar free peanut butter and always add about a half cup of coffee to thin it out a bit. Perfect every time
These are the best!!!
You have the Best Recipes Carolyn, thank you!
I can’t use Animal Collagen and wonder if you or any of your readers can recommend a Vegetarian option. Many thanks!
Can I make these with unflavored whey protein instead of chocolate flavored?
Yes, but you may need an additional tablespoon of cocoa powder for flavor.
Can I use unflavored collagen peptides? If so, would I add more cocoa powder?
Yes, you can use that. Add 1/2 tbsp more cocoa and a bit more sweetener too. You may also need a touch more liquid for the batter.
Sooooo gooood!!! I cannot get enough of these. They are devine ! So incredibly moist and delicious.
These muffins are the best chocolate muffins I have ever had. I have made them twice. The first time I had Chocolate Keto Collagen, but the 2nd time I only had unflavored collagen so I added one extra tablespoon of Valrhona Cocoa powder to give them more chocolate flavor. They were both good but using the chocolate collagen made them much better. They tasted like brownie muffins, and have become my go to chocolate muffin!
Seriously perfect. May add some greens powder next time, won’t be able to taste it!! I also used coconut sugar instead of sweetener.