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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.
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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
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
1Muffins 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
1I’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!