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GET IT NOWMy Protein Muffins Are Moist, Cakey, And Chocolaty Without Refined Sugar
These protein muffins are my double chocolate take on the ones I loved with a latte back in college. Back then, one of my favorite things in the world was a coffeehouse latte and a sugary muffin for breakfast (um, no wonder I had no energy). Like my low carb blueberry muffins, today’s double chocolate protein muffin recipe is inspired by those memories. But here’s why this one is better:
- Super moist, cakey crumb – Protein powder can dry out baked goods, but not here! I used a combination of collagen, almond flour, coconut oil, and Besti to keep the texture soft and moist. Say no to dry or rubbery protein muffins. Just no.
- Rich, double chocolate flavor, with other variations – I didn’t want to choose between chocolate protein muffins and chocolate chip protein muffins, so this recipe has both: deep chocolate flavor in the crumb and melty pockets throughout. But I’ve included other flavor options below.
- Easy one bowl recipe – This batter comes together without a mixer or a pile of dishes.
- High protein, low carb – My protein muffin recipe has 10 grams of protein and just 5 grams net carbs in each one, and no refined sugar. Plus, they’re gluten-free and dairy-free.
If you miss that coffeehouse muffin-and-latte combo like I do, these high protein muffins give you the same rich chocolate vibe. Except with ingredients and macros that can actually be a balanced, healthy breakfast (or snack).
Make them with me, and pair one with my protein coffee if you want an extra protein boost!
“OMG! 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.”
-Marilyn
Ingredients & Substitutions
Here I explain the best ingredients for my protein muffin recipe, what each one does, and substitution options. For measurements, see the recipe card.
- Collagen Protein Powder – This is my first choice for the moist, cakey texture in this recipe, and it’s what makes these high protein muffins. (I love collagen for protein cookie dough and protein cookies, too!) Whey protein powder can work, but is a little less forgiving with dryness, so be extra careful not to overbake. Other protein powders absorb liquid differently and create different textures, so I can’t guarantee they would work well.
- Wholesome Yum Blanched Almond Flour – I use this instead of the white, wheat, or oat flour I’ve seen in most other protein muffin recipes, because it’s low carb, gluten free, and provides some extra protein. Some brands can be too coarse, but this one I use is super-fine, so the muffins have a more delicate crumb and don’t turn out grainy. I don’t recommend coconut flour as a 1:1 swap here, because it’s much more absorbent and makes this batter too dry.
- 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. Avoid liquid options, such as maple syrup or honey, because the batter consistency will change too much.
- Cocoa Powder – I use and recommend unsweetened Dutch processed cocoa like this for a deeper chocolate flavor with less bitterness.
- Coconut Oil – For moisture and richness. 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 protein muffins more.
- Almond Milk – Thins out the batter. Feel free to substitute any milk you like. I’ve had success with regular dairy milk here, too.
- Eggs – Use whole, large eggs, or you can substitue flax eggs if needed.
- Baking Powder (for lift), Sea Salt (for balance), & Vanilla Extract (for flavor)
- Chocolate Chips – I use these sugar-free ones, and they give you the second half of the double chocolate situation. I fold most into the batter, but reserve a few for the tops.
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 the dry ingredients. In a large bowl, stir together the almond flour, Besti, cocoa powder, collagen protein powder, baking powder, and sea salt until evenly combined.
- Add the wet ingredients. Stir in the melted coconut oil and almond milk, then whisk in the eggs and vanilla. Fold in the chocolate chips last. I whisk the eggs in after the oil and milk, as they don’t scramble from the hot coconut oil this way.
- Fill the muffin cups. Divide the batter evenly among 12 lined muffin cups, filling them almost full. If you reserved some of the chocolate chips, press them gently into the tops.
- Bake the protein muffins. They’re ready when a toothpick inserted into the center comes out clean. Transfer to a cooling rack and let them cool for the best texture.
My Recipe Tips
- Whisk the dry ingredients really well. Cocoa powder and protein powder both like to clump. I like to mix them with a whisk to help break everything up. You can also use a sifter like this if you want to be extra sure.
- Use room temperature ingredients. This helps make a smooth, evenly mixed batter.
- The right sweetener is key for the best texture. I mentioned this, but can’t emphasize enough: Besti sweetener is what makes these muffins so moist. The only alternative that works the same way is plain granulated allulose sweetener, but you’d need more of it to get the same sweetness.
- Expect a thick batter. Think scoopable, not pourable. It’s much thicker than a traditional wheat-flour muffin batter, but resist the urge to thin it out!
- Don’t forget the muffin liners (and get the right ones). This protein muffin batter can stick to a bare pan or basic paper liners. I use these parchment muffin liners with this muffin tin for cleaner release.
- Be careful not to overbake. This is always important, but especially with high protein baking! These high protein muffins can go from moist to dry pretty quickly. I start checking toward the early end of the bake time and pull them as soon as a toothpick comes out clean. A few extra minutes can make a noticeable difference in how they taste.
- Let them cool to set the inside before eating. The crumb sets as the muffins cool, so I let them come to room temperature. You can always warm one again later if you prefer it warm.
Protein Muffins (Double Chocolate, No Sugar)
My protein muffins are super moist, rich, and double chocolate with melty chocolate chips and no refined sugar. Easy to make in one bowl!
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, Besti, cocoa powder, protein powder, 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.
LAST STEP: Leave a rating to help other readers, or tag me @wholesomeyum on Instagram. I’d love to hear from you!
Maya’s Recipe Notes
Serving size: 1 muffin
- Tips: Check out my recipe tips above to help you get the right batter consistency, clean release, and most importantly, the best texture.
- Variations: See my variations below for vanilla, blueberry, banana, and pumpkin options.
- Storage: Keep the muffins in an airtight container on the counter for up to 3-4 days. You can also refrigerate them for up to a week, but they dry out more that way.
- Reheat: If you like a warm muffin, you can reheat these briefly in the microwave or oven. I like to add a little butter on top so they don’t dry out.
- Freeze: Cool completely, wrap tightly, and freeze for up to 3 months.
I provide nutrition facts as a courtesy. Have questions about calculations or why you got a different result? Please see my nutrition policy.
Add Your Notes Your Notes
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Protein Muffin Recipe
Flavor Variations
Want to change up the flavor? Since cocoa powder affects both the sweetness and texture of the batter, I make a few other adjustments when I want protein muffins that aren’t chocolate:
- Vanilla – Replace the cocoa powder with 1/2 cup additional almond flour, reduce the Besti to 1/2 cup and the almond milk to 1/3 cup, and increase the vanilla extract to 2 teaspoons. You can keep the chocolate chips or leave them out, up to you!
- Blueberry – I make blueberry protein muffins the same as the vanilla version above, except I add 3/4 cup of blueberries (surprise, I know) and use 1 teaspoon of vanilla. If using frozen berries, I recommend adding them straight from the freezer without thawing, or they’ll bleed into the batter during baking.
- Pumpkin – Replace the cocoa powder with 1/2 cup additional almond flour, reduce the Besti to 1/2 cup, and replace the almond milk with 3/4 cup pumpkin puree. Add 1/2 tablespoon of pumpkin pie spice. You can also make my almond flour pumpkin muffins instead.
More High Protein Recipes
If you’re looking for more ways to add protein to your meals and snacks, try one of my other high protein recipes next:
169 Comments
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! With those adjustments they turned out perfect!
Jessica
0Thank you, I will try that next time!
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?
Wendy
0They are soo good! Great for when you feel like a treat or just wanting a muffin!
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.
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??
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!
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.
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?
Dan
0I did same thing but added some cream cheese for more fat and the flavor. They came great
Maya | Wholesome Yum
0Hi Diana, I haven’t tried that but you probably can.
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.
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!
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.
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?
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.
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.
Maya | Wholesome Yum
0Hi Debbie, Sorry, I haven’t tried that, so can’t say for sure.