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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’ll Love These Protein Muffins
- 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
This section explains how to choose the best ingredients for healthy protein muffins, what each one does in the recipe, and substitution options. For measurements, see the recipe card below.
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
This section shows how to make protein breakfast muffins with step-by-step photos and details about the technique, to help you visualize it. For full instructions, including amounts and temperatures, see the recipe card below.
- 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.
Tips For The Best Protein Muffins
Baking with protein can create different results than recipes with conventional flour, so follow these tips for best results.
- 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.)
Storage Instructions
- Store: You can keep protein muffins on the counter for a few days, or in the fridge for 7 to 10 days.
- Freeze: Cool completely, then cover tightly and freeze for up to 1 month. They are best reheated afterward (either in the microwave or a warm oven, with a little butter on top), but they will taste delicious no matter what.
More Protein Powder Desserts
Looking to sneak more protein into you treats? Try these recipes!
Tools I Recommend
- 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 Muffin Recipe
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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Ingredients
Tap underlined ingredients to see where to get them. Please turn Safari reader mode OFF to view ingredients.
Instructions
Tap on the times in the instructions below to start a kitchen timer while you cook.
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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.
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Recipe Notes
Serving size: 1 muffin
Nutrition facts are provided as a courtesy. Have questions about calculations or why you got a different result? Please see our nutrition policy.
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133 Comments
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!
Marleigh
0Delicious. I will definitely be making these muffins again.
Sharon Murray
0I was wondering if it would be ok not to add the protein powder to these since I don’t have any right now.
Wholesome Yum M
0Hi Sharon, Yes, you can omit the collagen peptides if you don’t have any.
Jessica
0For all the expensive ingredients, these turned out dry and not as sweet as I would have liked. Any suggestions? The subs I made were plain isopure protein powder and half of the coconut oil was replaced with butter because I ran out. I baked them for 24 mins. Thanks, Jessica.
Wholesome Yum M
0Hi Jessica, Feel free to increase the amount of sweetener to 3/4 of a cup if you prefer your muffins a little sweeter. To take care of the dryness, you can increase the coconut oil by another 1-2 tablespoons. I hope this helps!
Jessica
0Thank you, I will try that next time!
Jessica
0Thank you! With those adjustments they turned out perfect!
Jessica
0Is melted butter an acceptable sub for melted coconut oil?
Wholesome Yum M
0Hi Jessica, Yes, that will work great! Enjoy!
Jessica
0Is plain Whey Protein Powder an acceptable substitute for the Collagen Powder? These keto ingredients can add up quickly and I’d rather not buy another thing if I can avoid it..
Wholesome Yum M
0Hi Jessica, Yes that will work nicely in this recipe.
Jessica
0Thank you for replying 🙂
Northern Keto
0This is the best Keto recipe I have ever made. I would call them cupcakes. So rich, moist, and chocolatey. You certainly could not tell it is Keto. The only problem I have is sticking to one. I realized that a lot of my favorites are Wholesome Yum. You did it again!!
Erin
0Oh my goodness. These are so good. Thank YOU! I have a toddler who refuses to eat anything with protein, so it is a constant struggle. He devoured these and I don’t feel guilty because the ingredients are wholesome. I am also gluten free, so I was able to eat them with him as well. Hooray!
Sonya
0They are now cooling. The batter tasted bitter like typical low carb sweeteners do, so a lil disappointed. I used swerve and followed your conversion chart. Maybe they’ll mellow after cooling??
Wholesome Yum M
0Hi Sonya, I suggest you try these with Wholesome Yum Allulose as the sweetener. There is not cooling or bitter aftertaste with Wholesome Yum Allulose.
Jennifer
0Delicious! Taste like regular (non keto) muffins. I will definitely make these again. Yumm!!
Karen Cronin
0These are delicious! Approved by all 4 of our children, and tauted as “the best homemade muffins”! I’m going to check out the other muffin recipes on this page and see what other nutritious recipes I can make for our whole family!
Sandra Thompson
0Hey, I totally love this idea. I just started keto, and I personally just find it hard to find recipes I really really like. I used to just always make a box of protein muffins from Kodiak Cakes, but they are definitely not keto. Have you tried Kodiak Cakes before? If so, how does the texture/taste of your muffins compare?
Wholesome Yum M
0Hi Sandra, I don’t have any experience with that brand. Keto muffins (in general) are a bit denser than conventional wheat flour muffins. The flavor and nutrition are obviously much better in keto recipes. I highly recommend you give these muffins a try. I think you will be pleased with the result.
Deborah
0Hey, should I weigh my ingredients and use the grams you say for let’s say cacao powder or use the amount in cups you say? When I weigh 1/2 cup of my cocoa powder I get 30 g, not the number of grams you say for 1/2 cup? So what should I do ? Weigh my ingredients or use cups whatever the weight? Thx
Wholesome Yum M
0Hi Deborah, Ingredients can vary in weight. If the measurement is off by more than a small amount (like it is with the cocoa powder you mentioned) then I would switch to measuring with cups to make sure you are keeping the right ratios in the recipe. I hope this helps.
Wendy
0They are soo good! Great for when you feel like a treat or just wanting a muffin!
Kathryn
0I usually can’t stand with low-carb baked goods; HOWEVER, these are soooo yummy. As a vegetarian, I don’t eat Collagen, so I replaces the peptides with some flax seeds that I blended into a powder and it worked well!
My husband is so picky and detests low-carb things, but he actually really loves these too!
Margie Duerr
0Made these last night, and am SHOCKED at how good they are! Warm out of the oven with grass fed butter…HEAVEN. Thank you so much for everything you do! <3
Alecia Jackson
0The best keto muffin! I have tried many recipes for muffins and they either taste like eggs, cream cheese or sand! These are really good …. seriously!
Sunny
0What exactly IS the recipe for these? Like in how much of each ingredient? I can’t follow the vagueness of this post, I need it spelled out…. like what do you add to the collagen (how much collagen), etc?
Wholesome Yum M
0Hi Sunny, The amounts are listed in the recipe card. You may need to turn off reader mode to be able to see it.
Naomi
0Can I use olive oil, whole milk or half and half vs the oils and milk that you have listed? I’m not a fan of coconut oils nor almond milk. I use regular oils and milks.
Wholesome Yum M
0Hi Naomi, You can make those substitutions but the recipes would no longer be low carb or keto.
Dan
0Hi, I made and loved these. My wife wants to try a blueberry protein muffin. Do you have any recommendations for subbing out the cocoa powder for something? Thanks
Wholesome Yum M
0Hi Dan, You could replace the cocoa powder with whey protein powder. Let us know how they turn out!
Wanderingweed
0Seriously the best muffins ive ever made. I think next time i make them i will use this recipe for cupcakes.
Agata
0This looks yummy. Do you think I can substitute almond flour for coconut flour? If yes, what would be the amount? Thank you!
Wholesome Yum A
0Hi Agata, almond flour and coconut flour aren’t interchangeable. You might have better luck with sunflower seed flour.
Sarah E Wickliffe
0Hi, I’m curious – if I were hoping to double the protein per Muffin (20g more of a meal replacement for me) what would you advise? I know doubling the protein powder might throw off the delicate balance. But there must be a way to up that protein! Thank you!
Jennifer
0I have celiac so have to be gluten free. However, I also have a confirmed allergy to almonds. Whst flour substitute can i use in place of almond flour and is conversion equal?
Wholesome Yum A
0Hi Jennifer, many people use sunflower seed flour as a 1:1 substitute, but I haven’t tested it here.
Maria
0I made more of your recipes for my daughter, she’s trying to loose weight your recipes and the others’ comments help me a lot. Thank you so much!!
Dylan
0As I only had 1/3 cup of almond flour, I had to improvise a bit, so to keep carbs down, and fibre up, I added 1/3 cup of ground flaxseed and 1 1/3 cup of ground psyllium husk. I was concerned, but it all came together nicely!
I’m not a fan of the rich taste of unsweetened cocoa powder, so I only added 1 tbsp to the mixture and also added in 2 tbsp of keto maple syrup to give them a fudgy feel and to sweeten it up a bit more (I don’t like the aftertaste of too much erythritol)!
They are amazing. Thank you for this recipe!
With my switches each muffin has 4g net carbs, 24g fibre, 17g fat, 8g protein, and 258kcal. With all that fibre, I shall be eating these sparingly!!
Andrea Nugent
0I have Perfect Keto chocolate collagen powder with mct oil powder mixed in will that work for this?
Also will butter make the taste better than the coconut oil?
Excited to try these!
Wholesome Yum
0Hi Andrea, I haven’t tested that brand so I can’t say for certain. Butter or coconut oil both work here, but butter gives it a more classic muffin flavor if you tolerate dairy.
Sam
0The muffins are absolutely AMAZING!!! Actually, all your recipes are! I have already preordered your cookbook and can’t wait for it to be released. Thank you for helping me to find a balance of incorporating a few keto friendly sweets into my food plan.
Tracy Jackson
0I made these today. They are SO GOOD!!! Not to mention so easy to make. I didn’t have the protein peptides, so I used chocolate protein powder instead and they turned out PERFECT! I also used monk fruit instead of erythritol. My 16 year old grandson, 4 year old granddaughter, husband and myself thought they were FANTASTIC!! The flavor and texture are spot on! Thank you so much for an awesome recipe!! 😀 I will be making these often.
Julie
0I put all these ingredients into MyFitnessPal and it was about 20 net grams of carbs per serving, how did you calculate your net carbs??
Maya | Wholesome Yum
0Hi Julie, As stated on the recipe card we use the USDA Food Database, which is more reliable than any 3rd party calculator. Most likely MFP is including sweeteners in the carb count, which you can exclude. You can reliably use the nutrition info stated above.
Deborah
0Hello, Can I use almond meal or oat flour instead? In what quantities? Would adjustments need to be made for texture/taste? Is roasted or unroasted almond milk better? Can I replace the 3 whole eggs with 6 egg whites? What are the diameter and height of each muffin well? Do you recommend water or nut milk? Can I use vegan butter or sunflower oil instead of coconut oil? Thx
Wholesome Yum M
0Hi Deborah, Using all substitutions you are suggesting would greatly change the recipe, I don’t know if the muffins would turn out. I will do my best to try to answer your questions individually. Almond meal will produce a crumbly and bitter (if the skins are left on) muffin. I do not use oat flour, so I’m not sure what the outcome would be in this recipe. Either roasted or unroasted almond milk will work fine in this recipe. I used unroasted in the recipes, as it gives a more neutral flavor. Using only egg whites will significantly dry out the muffins. Using the egg yolks provides both structure and moisture to the recipe. If you would like to skip the coconut oil, then I think the vegan butter would work best. I hope this helps!
Season
0These were a game changer! I didn’t have peptide powder, so i used a whey protein isolate. Came out DELISH! I also used dark chocolate cocoa powder to intensify the chocolate flavor. Used a stevia blend baking sweetener, and vanilla almond milk, unsweetened because that’s what i had. Tastes like a regular muffin!
Danielle
0if you don’t want to use the Vital Proteins Collagen Peptides can you just go without it and continue baking? If not what do I do to make the muffins (keto) without the powder?
Maya | Wholesome Yum
0Hi Danielle, Protein powder is a pretty crucial component of this recipe so you’d need a different one if you want to skip it.
Diana I Villanueva
0Can you use a chocolate protein powder rather than collagen? also, sub out almond milk for heavy whipping cream or coconut milk?
Maya | Wholesome Yum
0Hi Diana, I haven’t tried that but you probably can.
Dan
0I did same thing but added some cream cheese for more fat and the flavor. They came great
Alexandra
0I followed the recipe exactly, but made them in a donut pan instead. They came out great!
Brandon Castro
0Thank you, I like this link .. because I want eat free gluten
Brittney H
0Just wondering if there is a way to make these lower in fat! They sound amazing.
Maya | Wholesome Yum
0Hi Brittney, Sorry, this is a low carb recipe and isn’t low fat.
Joanna Irvin
0Hi Maya, I have enjoyed some of the recipes so far. For this recipe, it calls for collagen peptides. I have Bulletproof Collagen Protein Powder. Is it okay to substitute in place of the peptides and if so, should I alter the recipe in any way?
Maya | Wholesome Yum
0Hi Joanna, I haven’t tried it, but in theory it should work.
Julee
0What a great chocolate fix. I happened to have Birch granular xylitol sweetener and used it. (I’m in the process of trying different sweeteners)- They are lighter than I expected and deliver deep chocolate flavor. I look forward to having these to share with my company who are not lo-carb but they are choco-holics! I think they will love them.
Marilyn Brennan
0Fabulous snack or that something extra to make a meal more filling. I love to keep these on hand in my freezer to take out as needed.
Judy
0Hi, I made these and they came out great but this is what I did..I did not use any collegian peptide. I followed it except for these differences…
I used MCT OIl for coconut oil. I added 1/3 cup of organic honey. I used 1/2 cup sugarfree chocolate chips and 1/2 cup walnuts. I used unsweetened almond/coconut milk. I had to cook them 5 mins longer but they are great.
Shannon Jacobson
0These tasted more like bran muffins than double chocolate. Will not make these again.
Bobbi J Flowers
0As a person who is allergic to coconut, can coconut oil be substituted with butter in your recipes? I leave alone any recipe with coconut flour. Thank you for your time.
Maya | Wholesome Yum
0Hi Bobbi, It depends on the recipe. Usually you can, but it’s best to ask for each one just in case. In these muffins either one will work.
Daniela
0I swapped out the coconut oil for butter. I haven’t made them with coconut oil so I can’t compare, but mine turned out soooo good!
Vicki Gambrell
0Can you use a multi-collagen protein powder?
Maya | Wholesome Yum
0Hi Vicki, Yes, that should work fine!
Marlien
0Great recipe! Tastes just like the best chocolate cake. I used coconut oil spray and a nonstick ceramic muffin pan instead of muffin papers. Worked out great, slightly chewy on the outside.
Maya | Wholesome Yum
0I am so happy to hear that, Marlien! Thank you!
Diane Kimes
0Can you use butter and milk instead of almond milk and coconut oil? Those aren’t things I usually have on hand, nor do I really want to use them for anything else, so fingers crossed…
Maya | Wholesome Yum
0Hi Diane, Yes, that should work fine!
Tracy
0What type (brand) of chocolate chips did you use? I have loved every recipe of yours that I have tried
Maya | Wholesome Yum
0Hi Tracy, I use these.
Nancy Nakae
0Hi! Can I leave out the collagen? Thanks!
Maya | Wholesome Yum
0Hi Nancy, No, sorry, that’s an important aspect of the recipe.
Heidi
0Does the collagen affect the way that the muffins stay together or the net carb count? Why are they important to the recipe? I don’t have this product and I’m not sure I’m comfortable using it, but my husband really wants some chocolate muffins.
Melissa
0Hi Heidi, The collagen affects the nutrition of the recipe. The carb count will remain the same, but it does add quite a bit of protein to the recipe (hence the name, hehe ). Enjoy!
Debbie
0Can you use whey protein powder instead of collagen peptides?
Maya | Wholesome Yum
0Hi Debbie, Sorry, I haven’t tried that, so can’t say for sure.
Valerie
0Can you use the Keto MCT oil Powder instead of the Collegon Peptides?
Maya | Wholesome Yum
0Hi Valerie, MCT oil powder has different properties, so the texture would be quite different. I haven’t tried to say for sure if it would work.
Alayssia Brown
0Hi Debbie, did you try? If so how did they turn out? I’m looking to make some with my whey protein powder! Thanks
Wanda
0Alayssia Brown, Yes it worked with Whey Protein Powder. so yummy.