Chocolate Protein Muffins Recipe

Name: Chocolate Protein Muffins Recipe (Healthy & Low Carb!)
Prep time: 10 min
Cook time: 25 min
Total time: 35 min
Ingredients: 2 cups Wholesome Yum Blanched Almond Flour; 1 cup Besti Monk Fruit Allulose Blend; 1/2 cup Cocoa powder; 1/4 cup Collagen protein powder; 1 1/2 tsp Baking powder; 1/4 tsp Sea salt; 1/3 cup Coconut oil ((melted)); 1/2 cup Unsweetened almond milk ((at room temperature)); 3 large Eggs ((at room temperature)); 1/2 tsp Vanilla extract; 3/4 cup Sugar-free dark chocolate chips

Jump to recipeA healthy low carb protein muffin recipe with just 10 minutes prep time! These easy protein powder muffins are moist, rich, and super chocolaty.

By Maya Krampf

132 Comments

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Before I went low carb 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… but much healthier.

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.

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.

Chocolate protein powder muffins with almond flour and Besti

Get Besti For This Recipe Here

What Are Protein Muffins?

Protein muffins have an added protein source that usually replaces some of the conventional flour in a traditional recipe.

Some protein powder 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!

Why You’ll Love This Chocolate Chip Protein Muffin Recipe

Rich, double chocolate flavor
Moist, cakey texture (NOT rubbery or dry!)
5 grams net carbs and 10 grams of protein 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?

Healthy protein muffin close up overhead

Ingredients You’ll Need

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.

Besti Monk Fruit Allulose Blend – Locks in moisture so these 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.
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.

Protein muffin recipe ingredients in bowls

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.

Protein muffin recipe batter with wet ingredients and chocolate chips added

Scoop. Transfer muffin batter to a lined muffin tin, filling cups evenly. Add additional chocolate chips on top, if desired.
Bake. Bake until an inserted toothpick comes out clean. Let muffins cool on a cooling rack for the best texture.

Finished protein powder muffins unwrapped and removed from baking pan

Tips For The Best High 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.

Frequently Asked Questions

Answering a few quick FAQs…

Are protein muffins good for you?

Not all easy protein muffin recipes are good for you, since they can still contain added sugar or starches you may want to avoid. But these low carb protein muffins are definitely good for you, with no sugar, grains, or artificial ingredients.

How to make protein muffins moist?

There are several things you can do to keep muffins more moist:

Use enough fat. Fat adds moisture, and keeps the muffins more satisfying.
Use the best sweetener. Besti sweetener helps muffins retain moisture.
Choose a better protein source. A collagen-rich protein source keeps the recipe more chewy and rich, instead of dry or rubbery.

Can I make protein muffins with whey?

Whey is a common ingredient choice for protein powder muffins, but it is not the best for flavor or texture. I recommend a collagen protein for better results! However, you can still try these with whey if that’s what you have.

Can I use coconut flour?

Sorry, no. The properties of coconut flour are too different from almond flour to suggest a replacement. If you have a nut allergy, sunflower seed meal might work, but the flavor and texture will be different.

Storage Instructions

Store muffins on the counter for a few days, or in the fridge for 7 to 10 days.

Can you freeze protein muffins?

Yes, you can! 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), but they will taste delicious no matter what.

More Protein Powder Desserts

Looking to sneak more protein into you treats? Try these recipes!

Tools To Make Protein Muffins

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.

Healthy Protein Muffin Recipe

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132 Comments

Jill F
0 February 12, 2023Reply

Very 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
0 February 7, 2023Reply

Is 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?
- Wholesome Yum D
  0 February 8, 2023Reply
  
  Hi Kelli, Unfortunately, I don’t have any recommendations for that.
- Janine Phipps
  0 February 10, 2023Reply
  
  You can easily substitute unsweetened applesauce for oil and egg whites for whole eggs to drastically reduce the calories!
Brenda
0 May 21, 2022Reply

Is 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
  0 May 23, 2022Reply
  
  Hi Brenda, There is a print recipe at the top of the recipe card.
  - Jess
    0 August 16, 2022Reply
    
    Made 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!
  - Yesenia
    0 January 18, 2023Reply
    
    I tried these tonight and they were delicious. I used Splenda Magic Baker because it was the only sweetener that I had on hand.
Lucelle
0 April 20, 2022Reply

Hi! 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
  0 April 21, 2022Reply
  
  Hi Lucelle, You can switch the US customary measurements to metric in the recipe card.
Vanessa
0 March 20, 2022Reply

Can you use coconut sugar instead of monk fruit in this recipe?
- Wholesome Yum D
  0 March 21, 2022Reply
  
  Hi Vanessa, Coconut sugar is not a low carb sugar so I don’t use it.
Shawna
0 March 2, 2022Reply

Hi there! Can I use whey protein instead of collagen?
- Wholesome Yum D
  0 March 2, 2022Reply
  
  Hi Shawna, Yes that should work for you!
Holly
0 February 22, 2022Reply

Amazing!
Tracy
0 January 26, 2022Reply

Could I skip cocoa powder and add vanilla and blueberries?
- Maya | Wholesome Yum
  0 January 26, 2022Reply
  
  Hi 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
0 January 11, 2022Reply

A 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
0 January 10, 2022Reply

Made 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
0 January 7, 2022Reply

Love 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
0 January 6, 2022Reply

Can I make these without collegin powder?
- Wholesome Yum D
  0 January 7, 2022Reply
  
  Hi Virginia, No, sorry, that’s an important aspect of the recipe.
Lori
0 December 22, 2021Reply

I’m diabetic must you use 1 cup of sweetener?
- Wholesome Yum D
  0 December 22, 2021Reply
  
  Hi Lori, Besti sweetener has zero calories, zero net carbs, and zero glycemic index.
Ellen
0 December 19, 2021Reply

Hello, can I use the monk fruit sweetener without the allulose for the chocolate muffins?
- Wholesome Yum D
  0 December 21, 2021Reply
  
  Hi 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
0 December 13, 2021Reply

What if you don’t want to use coconut oil?
- Maya | Wholesome Yum
  0 December 13, 2021Reply
  
  Hi Lori, You can use butter instead if you prefer.
Moop Brown
0 December 13, 2021Reply

I love that these muffins are protein filled, low-carb, and don’t take long to make. Can’t wait to try.
Heidy
0 December 12, 2021Reply

This is an amazing looking recipe that I bet my husband would love!! Thanks for the specific instructions and information! Happy Holidays!
Gwynn
0 December 12, 2021Reply

Very delicious and nutritious way to start the day!
Essie
0 December 11, 2021Reply

I would love to do vanilla! How would one go about that?
- Wholesome Yum D
  0 December 13, 2021Reply
  
  Hi Essie, I suggest checking out my Keto Chocolate Chip Muffins Recipe for a vanilla based muffin.
Lauren Michael Harris
0 December 11, 2021Reply

Double chocolate chip muffins are my absolute favorite! This healthier version fits in perfectly with my lower sugar diet. Great recipe!
Andrea Howe
0 December 10, 2021Reply

I 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
0 December 9, 2021Reply

I 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
0 December 9, 2021Reply

Yum! These were delicious! I love these types of protein muffin recipes! Perfect for a quick and healthy breakfast on busy mornings.
Amanda Dixon
0 December 8, 2021Reply

These 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
0 December 8, 2021Reply

Wow – what a creative way to use protein powder – an excellent breakfast idea or even post workout snack.
Marta
0 December 7, 2021Reply

I 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.