Chocolate Almond Flour Protein Muffins
Chocolate Almond Flour Protein Muffins that are healthy enough for the breakfast table and delicious enough for dessert. With over 11 grams of protein and all healthy ingredients, they're a muffin recipe that is truly the best of both worlds.


Yes, you can have your cake and eat it, too. (cause why the heck would you just sit around looking at it?) Only these ‘cakes' are chocolate protein muffins that are the most delicious things you'll ever meet yet somehow they manage to be good for you, too.
I don't know how they do it. They should be called Magic Muffins. Since they're packed with over 11 grams of protein in each muffin, we'll stick with calling them Protein Muffins. ← tell it how it is!
Why you need Chocolate Almond Flour Protein Muffins in your life:
- Coffee + chocolate dessert anything is just awesome. Hello, happy mornings.
- Your kiddies will gobble these up without complaint. Hello, even happier mornings.
- Weekday breakfast meal prep that will make you look like a rockstar.
- These protein muffins are double-duty desserts. Warm one up in your oven after dinner then pop a scoop of your favorite vanilla ice cream on top of it. ← please do this. you can thank me later.
- You're looking at the most delicious way to get your daily fix of Vital Proteins Collagen Peptides. Sure, you could put a scoop or two in your coffee or smoothie (as I often do) but adding it to your chocolate breakfast muffins just seems like a much better (and tastier) idea.
Watch the Chocolate Protein Muffins Video:
One of the best parts about these protein muffins is that they are ridiculously easy to make and virtually impossible to mess up.
Almond flour muffins, in general, tend to be very flexible recipes. I've made versions of my own paleo muffin recipes where I haven't measured anything and throw in random ingredients just for fun. (avocado, zucchini, cooked cauliflower, anyone?)
These protein muffins are no different.
Protein Muffins Step 1:
Gather your ingredients and mix them all together. And I'm hardly exaggerating.

Chocolate Protein Muffins Step 2:
The hardest part of your muffin making adventure will be deciding how long to bake them. Here are the guidelines:
- Super fudgy, soft in the center muffins that have dessert written all over them: 12-14 minutes.
- Firm muffins that hold their shape and pack well: 18-20 minutes.
Decisions are hard!
I like to aim for right in the middle and cook them for 16-17 minutes for muffins that are soft and a little delicate but can still (carefully) be kept on hand for grab and go breakfasts.

Step 3:
Decide whether you want to eat one of your magic creations right away …

Or top it with a scoop of vanilla ice cream …


It's kind of ridiculous that a chocolate muffin that looks that good could be healthy, too? #makesnosense
One of my favorite ‘tricks' for bumping up the protein in recipes is to add a few scoops of Vital Proteins Collagen Peptides. Not only do you get an extra 9 grams of protein per scoop, but you also get all the health benefits of collagen.
Collagen is super important for optimal health. Our grandparents use to get a lot more of it in their diets by making their own bone broths. In our fast-paced lifestyle filled with boneless, skinless chicken, we get very little collagen in our diets naturally.
It's why I take Vital Proteins Collagen Peptides. I started taking it religiously every day about a year ago and have noticed that my joints don't feel as sore after long runs. Vanity bonus: my skin, hair, and nails are so much better now, too!
Most days, I add 2 scoops to my coffee. ← I know that sounds SUPER weird but you can't taste it at all. But I also love to add it to recipes.
More Vital Proteins recipes
- Flourless Molten Chocolate Lava Cakes
- Super Creamy Almond Butter Latte
- Triple Berry Paleo Banana Bread with Lemon Glaze
- Sticky Paleo Ribs with Chocolate BBQ Sauce
- Curried Chicken Cauliflower Rice Soup
- Grab and Go Bacon and Egg Cups
See what I mean? Big-time love for Vital Proteins!

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Paleo Muffin Recipes:
- Paleo Apple Cinnamon Muffins
- Triple Chocolate Paleo Banana Muffins
- Coconut Almond Paleo Breakfast Muffins
- Paleo Blueberry Muffins

Chocolate Almond Flour Protein Muffins
If you love this recipe as much as we do, let us know with a 5-star rating!
Ingredients
- ⅓ cup coconut sugar
- ⅓ cup melted coconut oil
- 4 large eggs
- 1 tablespoon vanilla
- 2 cups almond flour
- ¾ cup cocoa powder
- ¼ cup 4 scoops Vital Proteins Mixed Berry Collagen Peptides (their unflavored version works, too!)
- 2 teaspoons baking powder
- ½ teaspoon sea salt
- ½ cup hot tap water
- ½ cup chopped dark chocolate or paleo chocolate chips
- ½ cup chopped pecans
- Optional: flaky sea salt to top the muffins
Instructions
- Preheat your oven to 350 degrees. Line a 12-cup muffin tin with liners.
- Add the coconut sugar, coconut oil, eggs, and vanilla to a large bowl and beat with electric beaters.⅓ cup coconut sugar, ⅓ cup melted coconut oil, 4 large eggs, 1 tablespoon vanilla
- Add the almond flour, cocoa powder, Vital Proteins Collagen Peptides, baking powder, and sea salt and beat until just combined. Add the hot water and carefully beat it into the batter. Fold in the chocolate and pecans.2 cups almond flour, ¾ cup cocoa powder, ¼ cup 4 scoops Vital Proteins Mixed Berry Collagen Peptides (their unflavored version works, too!), 2 teaspoons baking powder, ½ teaspoon sea salt, ½ cup hot tap water, ½ cup chopped dark chocolate or paleo chocolate chips, ½ cup chopped pecans
- Divide the batter between the lined muffin cups, filling them nearly to the top. For extra chocolaty muffins, top with a few chocolate chips or chunks.
- Bake the muffins for 12-20 minutes – see the guidelines below. Let the muffins cool for 5 minutes before removing them from the muffin tin. Optional: top with a little sprinkle of flaky sea salt.Optional: flaky sea salt to top the muffins
I made these for my family yesterday morning and everyone loved it! My family had eaten all of them by the time I went for seconds! I’m going to make them again today or tomorrow, and was wondering if I made a double batch if I could freeze some of the batter? These are definitely a new family favorite. Thank you!
They freeze really well!
Hello, I would really love to try these muffins but, don’t do commercially made protein powders. Do you know if any subs (dairy free) that I could use? Or maybe just add a bit more almond flour? Thank you, Mary Beth
You can simply omit the collagen if you like. 🙂
Delicious,I added frozen organic blueberries and used organic honey instead of sugar then once cooled cut in half added whipped cream mixed with 95% melted chocolate sprinkle with chopped pistachios, yum yum???
These are the best paleo muffins I’ve ever had. The flavor and consistency are perfect. We will definitely make them again!
That’s great, Michele! Thank you for the comment!
I’m wondering if you know how much fiber is in each muffin. I’m making them for my kids so that’s always something I like to know. 🙂 Thanks so much!
There are 2.7 grams. 🙂
Made these muffins several times, people at work and friends love them.
That’s so great to hear!
HI, will be trying these very soon…i just noticed that it says 3/4 cacao powder… its 3/4 cups i presume? Also, any substitute for the coconut sugar?
Yes! Thank you for catching that. It’s been updated now. I haven’t tried this recipe with anything other than coconut sugar before. Brown sugar would definitely work. A sugar alternative like erythritol would probably work, too. 🙂
These are fantastic! I have a wheat allergy and am always looking for treats that the whole family can enjoy. The texture was fantastic and they were very chocolatey which made for a happy husband and toddler here. Thank you for sharing! I will definitely make these again!
*I made these exactly as followed with zero changes*
I’m so happy to hear you enjoyed the recipe! Thank you for coming back to let us know!!
These muffins are the best! Will check out your other vp recipes for more inspo.
I’m happy to hear you like them as much as we do!
So for people like me who may or may not love chocolate. Would a full cup of chocolate chips be too much?
They are quite chocolaty. You can always cut down the amount. 🙂
I’m so glad you broke down the timing so you get your muffin exactly how you want. Fudgy muffins are life so I’m glad I know exactly how long much time is need!
Fudgy muffins are the best, aren’t they?!!
Muffins are my FAVE, especially blueberry or lemon poppyseed muffins! Chocolate muffins taste more like frosting-less cupcakes to me. Nothing wrong with that, but I find them more suitable for dessert than breakfast! However, I still wouldn’t turn down chocolate for breakfast. Thus, these muffins might just be calling for me to make them and dig in!
Exactly! These could totally be eaten as dessert!
Delicious, decadent and satisfying!
I’m so happy to hear you like them!!
Thank you for this awesome looking and healthy dessert recipe! Can’t wait to try it
You are so welcome!!
Dear Kristen,
Have been reading your blog for ages, though I confess I have never cooked any of your cakes.
The reason? I live in a metric world, plus your units like cups are volume-based (cup), not weight based (gram).
Therefore 1 cup of honey is not the same weight as a cup of sugar.
If I can still risk with your fusion salads or dishes, I need some guidance for the sweets.
In a nutshell, knowing that is never going to be precise,
How many grams in a cup?
Then, why do you still use coconut oil, though it is being denounced as harmful?
Thank you.
1 cup of almond flour is 96 grams – or at least that is what Google told me. This is a really flexible recipe so the exact amount isn’t super important.
I use coconut oil because it is a great dairy-free alternative to butter. If you are concerned about it, you could always use melted butter or a neutral flavored oil instead. 🙂
Thank you so very much!
You are welcome!
Hello! Can you make this without the collagen stuff or will it not bake right? I have all the other ingredients!
The recipe will work without the collagen, but you’ll miss out on the extra protein and other health benefits. Definitely worth picking up some Vital Proteins for your next batch!
Hi, Can I replace the collagen with my protein powder?
I have never tried baking with protein powder so I’m really not sure how it works in recipes.