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Before I went low carb/keto years ago, one of my favorite things in the world was a coffeehouse latte and a muffin for breakfast. In college, it was my favorite study snack – and no wonder I had no energy. Today’s double chocolate protein muffins recipe is inspired by those memories… made low carb, of course.
So much has changed since those days. But, even now – many years, two kids, and a business later – there’s something about enjoying a muffin with a steaming cup of keto coffee that’s just perfection. Except these days, it’s either keto blueberry muffins or low carb protein muffins.
I didn’t want to choose between chocolate protein muffins and chocolate chip protein muffins, so this recipe is both. Double chocolate protein muffins!
And I feel so much better eating them than I did after those coffeehouse ones.
Benefits of a Healthy Protein Muffin Recipe
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 that Vital Proteins Collagen Peptides are my all-time favorite.
So, while some protein muffin recipes use whey protein powder, I’m using collagen peptides in these.
This double chocolate protein muffin recipe was just another excuse to sneak in more collagen. And more chocolate (obviously!). And feel good about it for breakfast. đŸ˜‰
You’d never guess by the taste or appearance, but these low carb protein muffins are actually good for you! Without the sugar, without the carbs, and without the energy swings that you’d expect from traditional wheat-and-sugar muffins.
With only 5 grams net carbs and 10 grams of protein, this low carb high protein muffins recipe is a good balance between getting your protein in and being suitable for both low carb and keto lifestyles.
In fact, they are even paleo friendly if you use a suitable sweetener. I used allulose, which is natural, but if you prefer something else for a paleo version and don’t mind natural sugar, try coconut sugar.
The collagen in these healthy protein muffins not only keeps you full, it’s also the most abundant protein found in the body. It’s crucial for so many aspects of health, from skin and hair to joints and digestion. Check my article for a full list of amazing collagen benefits, as well as references.
Aside from all the obvious reasons for including collagen in my double chocolate protein muffins, it also has a surprising advantage for the recipe itself. The collagen protein kind of acts as a stand-in for gluten. Gluten (also a protein!) would have been found in wheat muffins, and of course is absent in our low carb protein muffins. So, the collagen fills in instead, improving the texture.
How To Make Chocolate Protein Muffins
The process for how to make chocolate protein muffins is actually very similar to my keto blueberry muffins. Stir together the dry ingredients, add the wet, whisk it all together. Fold in the chocolate chips, scoop into muffin liners and bake.
One bowl. Easy, peasy.
Just a few tips in case you need ’em…
Make sure your baking powder is fresh.
As with all low carb baking, fresh baking powder is crucial. If it’s stale, the double chocolate protein muffins won’t rise.
Choose your favorite granulated sweetener.
I used allulose. Don’t like it or have? No problem. Any granulated sweetener is fine.
However, don’t use a super concentrated sweetener (like pure stevia or pure monk fruit), or a liquid sweetener, because these will throw off the wet/dry ratio of the batter.
Check my low carb sweetener conversion chart if you want to use something other than allulose.
Expect the batter to be thick.
The batter for these low carb protein muffins might be thicker than some other muffin recipes you’re used to.
Here is what it looks like, to give you a visual:
Add extra chocolate chips on top.
This isn’t required, but something to note. If you want chocolate chips on top, you need to put chocolate chips or my keto chocolate bar (chopped into small pieces) on top! I added them on top after filling the muffin cups for a nicer appearance.
Let the muffins cool if you can.
These chocolate protein powder muffins are very moist inside, almost like a cross between a muffin and a brownie. So, just like a good brownie, it’s best to let them cool before eating.
If you like warm muffins, like I do, simply reheat when ready to eat.
Eating your healthy protein muffins right away won’t be a total deal breaker, but the texture is just better if they cool first.
How To Store Low Carb Protein Muffins
You can store low carb protein muffins on the counter for a few days, or increase their shelf life in the fridge. They’ll last about 7 to 10 days in the fridge.
Can You Freeze Protein Muffins?
Yes, you can! Go ahead and stick ’em in the freezer once they’ve cooled to room temperature.
They are best reheated afterward. Which is totally the best way to enjoy double chocolate protein muffins, anyway.
More Keto Chocolate Recipes
- Sugar-free Chocolate Pudding
- Keto Mint Chocolates
- Chocolate Protein Pancakes
- Keto Chocolate Peanut Butter Smoothie
Low Carb Double Chocolate Protein Muffins Recipe:
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Low Carb Double Chocolate Protein Muffins Recipe
These low carb double chocolate protein muffins are easy to make, moist & delicious. This healthy protein muffin recipe needs just 10 minutes prep time!
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GET BESTIInstructions
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 peptides, 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 golden and an inserted toothpick comes out clean.
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Recipe Notes
Serving size: 1 muffin
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92 Comments
Kendall Boone
these are amazing…just what my choco crave needed
thank you,
rebecca
I’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
Hi 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
This 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
If 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
Hi 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
Delicious!
Marleigh
Delicious. I will definitely be making these muffins again.
sharon murray
I 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
Hi Sharon, Yes, you can omit the collagen peptides if you don’t have any.
Jessica
For 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 if the coconut oil replaced with butter because I ran out.
I baked them for 24 mins.
Thanks,
Jessica
Wholesome Yum M
Hi 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
Thank you, I will try that next time!
Jessica
Thank you! With those adjustments they turned out perfect!
Jessica
Is melted butter an acceptable sub for melted coconut oil?
Wholesome Yum M
Hi Jessica, Yes, that will work great! Enjoy!
Jessica
Is 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
Hi Jessica, Yes that will work nicely in this recipe.
Jessica
Thank you for replying đŸ™‚
northern keto
This 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
Oh 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
They 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
Hi Sonya, I suggest you try these with Besti Allulose as the sweetener. There is not cooling or bitter aftertaste with Besti allulose.
Jennifer
Delicious! Taste like regular (non keto) muffins. I will definitely make these again. Yumm!!
Karen Cronin
These 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
Hey, 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
Hi 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
Hey, 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
Hi 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
They are soo good! Great for when you feel like a treat or just wanting a muffin!
Kathryn
I 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
Made 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
The 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
What 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
Hi Sunny, The amounts are listed in the recipe card. You may need to turn off reader mode to be able to see it.
Naomi
Can 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
Hi Naomi, You can make those substitutions but the recipes would no longer be low carb or keto.
Dan
Hi, 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
Hi Dan, You could replace the cocoa powder with whey protein powder. Let us know how they turn out!
Wanderingweed
Seriously the best muffins ive ever made. I think next time i make them i will use this recipe for cupcakes.
Agata
This 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
Hi Agata, almond flour and coconut flour aren’t interchangeable. You might have better luck with sunflower seed flour.
Sarah E Wickliffe
Hi, 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
I 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
Hi Jennifer, many people use sunflower seed flour as a 1:1 substitute, but I haven’t tested it here.
Maria
I 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
As 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
I 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
Hi 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
The 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
I 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!! đŸ˜€ I will be making these often.
Julie
I 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
Hi 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
Hello
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 by 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
Hi 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
These 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
if 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
Hi 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
Can you use a chocolate protein powder rather than collagen? also, sub out almond milk for heavy whipping cream or coconut milk?
Maya | Wholesome Yum
Hi Diana, I haven’t tried that but you probably can.
Dan
I did same thing but added some cream cheese for more fat and the flavor. They came great
Alexandra
I followed the recipe exactly, but made them in a donut pan instead. They came out great!
Brandon Castro
Thank you, I like this link .. because I want eat free gluten
Brittney H
Just wondering if there is a way to make these lower in fat! They sound amazing.
Maya | Wholesome Yum
Hi Brittney, Sorry, this is a low carb recipe and isn’t low fat.
Joanna Irvin
Hi 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
Hi Joanna, I haven’t tried it, but in theory it should work.
Julee
What 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
Fabulous 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
Hi, 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
These tasted more like bran muffins than double chocolate. Will not make these again.
Bobbi J Flowers
As a person who is allergic to coconut, can the 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
Hi 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
I 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
Can you use a multi-collagen protein powder?
Maya | Wholesome Yum
Hi Vicki, Yes, that should work fine!
Marlien
Great 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
I am so happy to hear that, Marlien! Thank you!
Diane Kimes
Can 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
Hi Diane, Yes, that should work fine!
Tracy
What type (brand) of chocolate chips did you use? I have loved every recipe of yours that I have tried
Maya | Wholesome Yum
Hi Tracy, I use these.
Nancy Nakae
Hi! Can I leave out the collagen? Thanks!
Maya | Wholesome Yum
Hi Nancy, No, sorry, that’s an important aspect of the recipe.
Heidi
Does 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
Hi 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
Can you use whey protein powder instead of collagen peptides?
Maya | Wholesome Yum
Hi Debbie, Sorry, I haven’t tried that, so can’t say for sure.
Valerie
Can you use the Keto MCT oil Powder instead of the Collegon Peptides?
Maya | Wholesome Yum
Hi 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
Hi Debbie, did you try? If so how did they turn out? I’m looking to make some with my whey protein powder! Thanks
Wanda
Alayssia Brown, Yes it worked with Whey Protein Powder. so yummy.