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Free Printable: Low Carb & Keto Food List
Get It NowYears ago, one of my favorite things in the world was a coffeehouse latte and a sugary muffin for breakfast. In college, it was my favorite study snack – and no wonder I had no energy. Like my low carb blueberry muffins, today’s double chocolate protein muffins recipe is inspired by those memories… but much healthier.
I didn’t want to choose between chocolate protein muffins and chocolate chip protein muffins, so this recipe is both. And I feel so much better eating them than I did after those coffeehouse ones.
Why You Need My Protein Muffin Recipe
- Rich, double chocolate flavor
- Moist, cakey texture (NOT rubbery or dry!)
- 10 grams of protein and 5 grams net carbs per muffin
- Prep in one bowl & bake in less than 30 minutes
- The perfect snack or filling breakfast
- Creates naturally keto and gluten-free muffins!
- Double chocolate… need I say more?
Baking with protein can create some dry results, but there’s a surprisingly simple solution: The sweetener! I use Besti Monk Fruit Allulose Blend because it measures just like sugar and locks in moisture — so you get a perfectly sweet muffin without the sugar spike.
Ingredients & Substitutions
Here I explain the best ingredients for my healthy protein muffins recipe, what each one does, and substitution options. For measurements, see the recipe card.
Some protein muffin recipes use ingredients like Greek yogurt, oat flour, banana, or gluten-free flour, but this recipe uses low carb ingredients to keep them higher in protein and lower in sugar!
- Besti Monk Fruit Allulose Blend – Locks in moisture, so these high protein muffins stay moist and sugar-free! You can make them with another sweetener if you must, but know that they will turn out more dry.
- Wholesome Yum Almond Flour – Another natural source of protein that keeps this recipe gluten free. The fine grind delivers a texture closer to traditional flour! Avoid using almond meal, or almond flour brands that are coarser. Coconut flour is too dry and does not make a good substitute, but if you have a nut allergy, sunflower seed meal might work.
- Collagen Protein Powder – If you’ve seen my protein cookie dough bites or peanut butter protein cookies, you know I’m a huge fan of using collagen protein powder in low carb recipes. And this neutral powder makes a moist, cakey muffin, too. I prefer it over whey protein powder, but technically any unflavored protein powder will work in this recipe.
- Cocoa Powder – A must for easy chocolate protein muffins! Cocoa powder imparts a richer chocolate flavor than using melted chocolate. Make sure it’s unsweetened, and I typically recommend Dutch processed cocoa powder, which is less bitter.
- Baking Powder – Helps the muffins rise. Make sure it is fresh for best results. Don’t use baking soda, which is not the same and will yield a result that is bitter and does not rise.
- Sea Salt – Balances the sweet taste in the muffins.
- Coconut Oil – Keeps the muffins moist. You can also use butter or ghee. I don’t recommend substituting liquid oils, such as avocado oil, as this will change the texture of the end result.
- Unsweetened Almond Milk – Helps the batter reach the right consistency. Feel free to substitute with your favorite keto milk, or make homemade almond milk. Make sure it’s at room temperature, to avoid solidifying the coconut oil when mixing.
- Eggs – Use whole, large eggs, at room temperature for the same reason as the almond milk. Flax eggs might work for an egg-free option, but I have not tested this to confirm.
- Vanilla Extract – Use the best quality vanilla you can.
- Sugar-Free Chocolate Chips – Turns these into chocolate chip protein muffins! You can also use a chopped sugar-free dark chocolate bar.
How To Make Protein Muffins
I have step-by-step photos here to help you visualize the recipe. For full instructions with amounts and temperatures, see the recipe card.
- Mix dry ingredients. Mix almond flour, Besti, cocoa powder, baking powder, salt, and protein powder in a large mixing bowl.
- Add wet ingredients. Stir in melted coconut oil and almond milk, followed by eggs and vanilla. Fold in chocolate chips.
- Scoop. Transfer muffin batter to a lined muffin tin, filling cups evenly. Add additional chocolate chips on top, if desired.
- Bake. Bake the protein muffins until an inserted toothpick comes out clean. Let them cool on a cooling rack for the best texture.
My Recipe Tips
- Expect a thick batter. It will be thicker than traditional muffin recipes, but this is normal.
- Use the right sweetener. To avoid a dry muffin, use a an allulose-based sweetener, like Besti, instead of sugar alcohols such as erythritol. (Most brands of monk fruit and stevia also are erythritol-based. Besti is not, and keeps baked goods moist.)
- Cool completely. The texture is better this way, but you can easily warm them up later.
- Add chocolate chips in the batter and on top. It’s optional, but makes them look extra nice.
Recipe Variations
Want a different flavor? Try some of these other flavor variations:
- Banana – Make banana protein muffins by replacing the cocoa powder with 1 mashed ripe banana and an extra 1/4 cup of almond flour. Reduce the almond milk to 1/4 cup.
- Blueberry – Replace the cocoa powder with 1/2 cup additional almond flour, omit the chocolate chips, and add 1 cup of fresh or frozen blueberries to the batter to make blueberry protein muffins. (You can also try my almond flour blueberry muffins instead.)
- Pumpkin – Replace the cocoa powder with 1/2 cup additional almond flour, replace the almond milk with 3/4 cup of pumpkin puree, and add 1/2 tablespoon of pumpkin pie spice. You can use the chocolate chips or omit them. (Or, try my almond flour pumpkin muffins instead.)
More Protein Powder Desserts
Looking to sneak more protein into you treats? Try these recipes!
Tools I Use For This Recipe
- Muffin Tin – Can’t make muffins without one! I like that this one cleans easily if any batter gets outside the liners.
- Parchment Muffin Liners – Nothing sticks to these. Don’t confuse them with regular paper liners; the parchment ones are much better.
Protein Muffins (Healthy & No Refined Sugar)
These easy protein muffins are moist, rich, super chocolaty, healthy and refined sugar free! They are quick to prepare and need just one bowl.
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Instructions
Tap on the times in the instructions to start a kitchen timer.
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Preheat the oven to 350 degrees F (177 degrees C). Line a muffin pan with 12 parchment paper liners or silicone muffin liners.
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In a large bowl, stir together the almond flour, sweetener, cocoa powder, collagen, baking powder, and sea salt.
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Stir in the melted coconut oil and almond milk. Whisk in the eggs and vanilla. Fold in the chocolate chips last. (If you'd like, you can reserve 1/4 cup of the chocolate chips to add on top.)
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Scoop the batter evenly into the muffin cups, filling almost full. If you reserved some chocolate chips in the previous step, sprinkle them on top and press gently into the batter.
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Bake for about 25 minutes, until the tops are slightly darker on the edges and an inserted toothpick comes out clean.
Did You Like It?
Leave a rating to help other readers (this also helps me continue to provide free recipes on my site), or get the recipe sent to your inbox.
Maya’s Recipe Notes
Serving size: 1 muffin
- Tips: Check out my recipe tips above to help you get moist, perfectly textured muffins with just the right amount of sweetness!
- Store: Keep on the counter for a few days or in the fridge for up to 10.
- Freeze: Cool, wrap tight, and freeze for a month. Reheat for the best texture—microwave or warm in the oven with a little butter!
I provide nutrition facts as a courtesy. Have questions about calculations or why you got a different result? Please see my nutrition policy.
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Protein Muffin Recipe
169 Comments
Marilyn Cohen
1OMG! I cannot wait to get up every morning and have one of these with coffee. That is my breakfast. They put me in such a good mood. I make two dozen at a time and freeze them. And then I microwave it for 20 seconds. In love with a protein muffin. Thank you so much for this recipe. So chocolatey.
Maya | Wholesome Yum
0Awww, thank you, Marilyn! They do make an awesome breakfast!
Carol
1Omgosh these are amazing! I’ve tried many other low-carb muffin recipes and been disappointed with the results. Not so with these. They’re full of flavor, don’t have any aftertaste and fulfills my chocolate cravings. I used baking cocoa as that’s what I had on hand and after doing some research, there’s not much difference other than Dutch chocolate being a richer, dark chocolate flavor. We’re having these for dessert with our friends this weekend. That should speak volumes as to how good they are. I will definitely make these again. Thanks for a great recipe!
Traci
0Is it possible to make these egg-free? If, so, how?
Maya | Wholesome Yum
0Hi Traci, I covered this in the substitutions section above.
Jan
0These are fantastic! Very chocolatey and I love it! Wrapped in plastic wrap and froze so I can get one out each day.
Wholesome Yum D
0That’s great, Jan! I’m so happy you loved them. Freezing them individually is such a smart idea and perfect for a daily treat!
Sue Miller
0Do I really need the collagen powder? Is it a necessary ingredient?
Maya | Wholesome Yum
0Hi Sue, Yes, it’s a necessary ingredient to make these high protein muffins. You can use a different protein powder if you like. If you don’t need them to be high protein, you can use the search bar at the top to search “muffins” and find my other muffin recipes. Hope this helps!
Deborah Carr
0Omg!!! These taste so good! I make 2 dozen and freeze them too! 😋
Wholesome Yum D
0I love hearing that, Deborah! Freezing a batch is such a smart move, perfect for easy snacks later. So glad you’re enjoying them!
AKay
0These are VERY sweet made as is. Half the sweetener is much better.
Maya | Wholesome Yum
0Thank you for the feedback! Just to confirm, you used the same sweetener?
Marie L Wadleigh
0Please let me know if I can use a different kind of protein ingredient for the protein muffins, I have several kinds but not the one that you mention in your recipe, and I don’t know if the difference will make a big difference and I really can’t afford to buy another kind, I have collagen peptides, multi protein powder, and whey protein concentrate, very confusing for me, thanks.
Maya | Wholesome Yum
0Hi Marie, The whey protein concentrate you have should work in this recipe! It’s very similar to whey protein isolate that I used, it’s just a little higher in carbs, fat, and lactose whereas the isolate is more pure protein.
Rainbow Mermaid
0Muffins turned out amazing! I used chocolate collagen custard powder and added walnuts, but everything else was as written. They turned out so delicious!! I’ve been having one every day in place of a meal. They’re extremely filling. Thank you so much for all of the effort you put into creating delicious, healthy recipes for us! 🫶🏼🪻🩷
Maya | Wholesome Yum
0I’m so happy you liked them, thank you! Hope you make them again soon.
Tobias
0The consistency gets all weird.
Maya | Wholesome Yum
0Sorry to hear that, Tobias! Can you describe it a bit more? Did you make any substitutions? I’m happy to help troubleshoot if you can provide more detail.
George Burnetz
0These muffins taste great, are easy, and filling.
Maya | Wholesome Yum
0Thank you, George! Enjoy!
Ann
0I made these protein muffins yesterday. They were very yummy. Then I decided to put them in a small bowl of heavy cream…OMGOODNESS!!! Can’t wait to eat more 😋
Maya | Wholesome Yum
0I’m so glad you liked these protein muffins, Ann! Thank you!
Nikki H
0Hello!
Thanks for the recipe, I made it to support my macro diet. I was shocked though when I saw in the nutrition information that there is 20g of fat per serving. Is that wrong? The amount of coconut oil and eggs etc, divided among 12 muffins doesn’t seem like it could possibly fit 20g of fat into a single muffin. The coconut oil alone divided among 12 muffins equals ~1g fat per muffin. I wanted to ask about this because otherwise I can’t eat the muffins right now as I clearly don’t understand where all the fat is coming from haha. Thank you!
Maya | Wholesome Yum
0Hi Nikki, Most of the fat comes from the almond flour and coconut oil. Almond flour is made from almonds, so it’s not low fat, but it’s healthy, unprocessed fats. Hope this helps!
Rebecca
0Is there a way to use coconut flour instead of almond? Thank you!
Wholesome Yum D
0Hi Rebecca, Coconut flour is too dry and does not make a good substitute.
Lizzy
0We are unable to get Monk Fruit Allulose but I have erythritol, any suggestions for using this and not having the muffins come out dry?
Wholesome Yum D
0Hi Lizzy, You can use my Sweetener Conversion Chart to get the correct amount of erythritol to use in this recipe.
peh3420@Yahoo.com
0Do you have to use the Chips
Wholesome Yum D
0Hi, You can omit the chocolate chips if you want.
Agata
0Hi Maya. Could I substitute an almond milk with extra creamy unsweetened oatmilk?
Wholesome Yum D
0Hi Agata, Yes, that would work.
Judy
0Hi Maya,
I am so excited to see that you have updated this recipe! I used to LOVE these muffins. And then I started getting a lot of digestive problems with erythritol. I had to eliminate lots of foods from my diet.
Today, I looked at all the recipes like this that I just couldn’t toss. I was hoping someday there would be an improvement type of ingredient. I Put them in a notebook and put them away. Sadly.
I was absolutely thrilled to see that you are updating the recipe to use allulose and monkfruit. I am happy to try an old friend!
I’m going to try to make six muffins to test out how I do.
Thank you very very much
Judy
Beth Aschliman
0Do I have to use the collagen powder for these to turn out right?
Wholesome Yum D
0Hi Beth, Yes, you need include the collagen powder.
Nina
0What a solid recipe! Subbed equal parts applesauce for coconut oil and even reduced the sweetener to 1/2 cup and it turned out just sweet enough! Thank you for sharing because I’ll definitely be making these again.
Jill F
0Very good!! Chocolaty cake-like muffins. I used most of the recommended brands for ingredients and followed as written. My only wish was that the coconut oil could be substituted for something low in saturated fats. Otherwise, using monk fruit based sweetener and monk fruit based chips gives it lots of fiber!! I would definitely make again!
Kelli O'Neal
0Is there anyway to cut down the calories? I am finding in looking up high protein low carb muffin recipes that most are that way. Suggestions?
Janine Phipps
0You can easily substitute unsweetened applesauce for oil and egg whites for whole eggs to drastically reduce the calories!
Wholesome Yum D
0Hi Kelli, Unfortunately, I don’t have any recommendations for that.
Brenda
0Is there a way to print a condensed recipe out from your site? I can’t figure it out and I don’t want to print a ton of pages. Thanks.
Wholesome Yum D
0Hi Brenda, There is a print recipe at the top of the recipe card.
Yesenia
0I tried these tonight and they were delicious. I used Splenda Magic Baker because it was the only sweetener that I had on hand.
Jess
0Made these tonight and they are delish! I only had the chocolate collagen and it has stevia. My only changes were to cut back on the cocoa powder since I had choc in the collagen and I don’t have the special sweetener so I just added maybe 1/3 c honey (I’m not Keto) to taste. For milk, I used unsweetened coconut bc it was all I had. I’m going to serve them tomorrow with peanut butter on top!
Lucelle
0Hi! Thank you for all the wonderful recipes I’d like to use the metric measurement for your recipes instead of cups, is it accurate?
Wholesome Yum D
0Hi Lucelle, You can switch the US customary measurements to metric in the recipe card.
Vanessa
0Can you use coconut sugar instead of monk fruit in this recipe?
Wholesome Yum D
0Hi Vanessa, Coconut sugar is not a low carb sugar so I don’t use it.
Shawna
0Hi there! Can I use whey protein instead of collagen?
Wholesome Yum D
0Hi Shawna, Yes that should work for you!
Holly
0Amazing!
Tracy
0Could I skip cocoa powder and add vanilla and blueberries?
Maya | Wholesome Yum
0Hi Tracy, You wouldn’t be able to simply omit the cocoa powder, because it would throw off the batter consistency and ratios in the recipe (and replacing it with vanilla and blueberries would not help with this). I do have blueberry muffins here you can make instead. Hope this helps!
Susan
0A post script to what I wrote yesterday: today I put our muffins into the microwave and warmed them slightly. They were even better slightly warm, and they tasted wonderfully chocolatey. Also, they tasted perfectly sweet. Despite not using allulose, they were still nicely moist.
Susan
0Made these today so we could have some good snacks, and they turned out very nice. I expected them to be sweeter than they are (but I’m not big on seriously sweet). I was also impressed with how beautifully they rose. I used a monk fruit/erythritol sweetener, because I am really wary about using allulose, and they came out nicely moist. This is a definite keeper recipe.
Denise
0Love this recipe. I did substitute 1/2c of lupin flour for 1/2 c of the almond flour, they taste like cupcakes. I’m going to have to hide them from my husband. Thank you for such a great recipe.
Virginia
0Can I make these without collegin powder?
Wholesome Yum D
0Hi Virginia, No, sorry, that’s an important aspect of the recipe.
Lori
0I’m diabetic must you use 1 cup of sweetener?
Wholesome Yum D
0Hi Lori, Besti sweetener has zero calories, zero net carbs, and zero glycemic index.
Ellen
0Hello, can I use the monk fruit sweetener without the allulose for the chocolate muffins?
Wholesome Yum D
0Hi Ellen, I recommend using Besti because it makes the muffins super moist. I cover alternatives in the post above, but other brands of monk fruit will generally yield a more dry result.
Lori Diefenderfer
0What if you don’t want to use coconut oil?
Maya | Wholesome Yum
0Hi Lori, You can use butter instead if you prefer.
Moop Brown
0I love that these muffins are protein filled, low-carb, and don’t take long to make. Can’t wait to try.
Heidy
0This is an amazing looking recipe that I bet my husband would love!! Thanks for the specific instructions and information! Happy Holidays!
Gwynn
0Very delicious and nutritious way to start the day!
Essie
0I would love to do vanilla! How would one go about that?
Wholesome Yum D
0Hi Essie, I suggest checking out my Keto Chocolate Chip Muffins Recipe for a vanilla based muffin.
Lauren Michael Harris
0Double chocolate chip muffins are my absolute favorite! This healthier version fits in perfectly with my lower sugar diet. Great recipe!
Andrea Howe
0I needed a good muffin recipe for my kids breakfast before school, and this one was perfect. Full of protein and healthy fats, they loved how chocolaty and moist they were! And I loved knowing I was giving them a nutritious breakfast 🙂
Susan
0I love that you use collagen protein powder in this recipe! I always stir some into my tea and coffee, and even my yogurt, but never thought to bake with it. I can’t wait to try this recipe.
Liz
0Yum! These were delicious! I love these types of protein muffin recipes! Perfect for a quick and healthy breakfast on busy mornings.
Amanda Dixon
0These muffins are delicious! The extra dose of protein made them nice and filling, and I just loved how chocolatey and moist they turned out.
Heather
0Wow – what a creative way to use protein powder – an excellent breakfast idea or even post workout snack.
Marta
0I don’t know how people can say that keto recipes don’t taste like conventional ones. Well, yes I can. This chocolate protein muffin didn’t taste anything like the conventional recipe. It tasted TONS better. I think these will replace my regular chocolate muffins from now on.
Kendall Boone
0These are amazing…just what my choco crave needed. Thank you.
rebecca
0I’ve used this recipe many times and I love it, today I was feeling ambitious and tripled the recipe….it didn’t turn out whatsoever very dry batter, I had to throw it all out. what did I screw up on? thoughts lol
Wholesome Yum M
0Hi Rebecca, Did you adjust the servings to 36 muffins or mentally scale up as you go? The recipe should work fine when scaled up.
Dani
0This recipe is FANTASTIC! I don’t have any collagen at home, so I made it with a chocolate powdered protein drink (pea protein and whey protein) I had in the cupboard. I cut the choc chips down to ½ cup and added a generous ½ cup of coarsely chopped walnuts. It was hard to add all that coconut oil (fat worries…, I know, old habits die hard) but I figured you had done the experiment and this is what worked, so I did it. I put a walnut half on each “muffin” (ha ha, we all know these are cupcakes…) for decoration.
Despite overcooking them a bit (got lost in a book and lost track of time), they came out great. I had one this AM, and it tasted like a yummy, large, fudgy brownie. This really impressed me, because I’ve never gotten an actual keto brownie recipe to work for me. This would also make a great birthday cake. Because of all the baking powder, they were not overly dense, and each cupcake had a mountain that rose up with the walnut on top–very appealing. Just the thing to grab on my way out the door to work, and feel good that I have this delicious confection to eat while snubbing the donuts people bring in.
For the people who thought this recipe was too dry, it’s important to aerate the almond flour and to use a separate spoon to put into the measuring cup without packing the flour at all. I then sifted all the dry ingredients so that they’d blend well, and whisked them again in the bowl. I think this is why they weren’t dry (in addition to all that coconut oil…).
Jane
0If I wanted to make a vanilla version of these and I have been using whey protein isolate instead of collagen, would I just increase the whey protein the same amount of the cocoa? Not exactly sure how that would work.
Wholesome Yum M
0Hi Jane, I’m not sure how that would work out either. It may be okay, or it may turn out rubbery depending on the brand of protein you are using. The textures can vary a lot. If you are interested, I do have a Chocolate Chip Muffin recipe here that may give you the flavors you are looking for.
Mylene
0Delicious!