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.

Chocolate Almond Flour Protein Muffins with a little sea salt sprinkled on top sitting on a blue background.

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.

All the ingredients for these protein muffins laid out on a blue and white table.

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.

A muffin tin filled with chocolate protein muffins fresh out of the oven with some almonds and pecans scattered around them.

Step 3:

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

A hand holding a still warm chocolate protein muffin with sea salt sprinkled on top.

Or top it with a scoop of vanilla ice cream …

A chocolate protein muffin with a scoop of melting vanilla ice cream on top.

A chocolate protein muffin cut in half with the chocolate chips inside still warm and melty.

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

See what I mean? Big-time love for Vital Proteins!

Chocolate Almond Flour Protein Muffins in a muffin tin with almonds and pecans sprinkled around.

Paleo Muffin Recipes:

Chocolate Almond Flour Protein Muffins with a little sea salt sprinkled on top sitting on a blue background.

Chocolate Almond Flour Protein Muffins

  • Author: Kristen Stevens
  • Prep Time: 10 mins
  • Cook Time: 20 mins
  • Total Time: 30 minutes
  • Yield: 12 muffins 1x
  • Category: Breakfast
  • Cuisine: American


Chocolate Almond Flour Protein Muffins that are healthy enough for the breakfast table and delicious enough for dessert. They're a muffin recipe that is truly the best of both worlds.



  • 1/3 cup coconut sugar
  • 1/3 cup melted coconut oil
  • 4 large eggs
  • 1 tablespoon vanilla
  • 2 cups almond flour
  • 3/4 cup cocoa powder
  • 1/4 cup (4 scoops) Vital Proteins Mixed Berry Collagen Peptides (their unflavored version works, too!)
  • 2 teaspoons baking powder
  • 1/2 teaspoon sea salt
  • 1/2 cup hot tap water
  • 1/2 cup chopped dark chocolate or paleo chocolate chips
  • 1/2 cup chopped pecans
  • Optional: flaky sea salt to top the muffins


  1. Preheat your oven to 350 degrees. Line a 12-cup muffin tin with liners.
  2. Add the coconut sugar, coconut oil, eggs, and vanilla to a large bowl and beat with electric beaters.
  3. 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.
  4. 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.
  5. 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.


Fudgy dessert muffins: 12-14 minutes. Soft and delicate muffins that hold their shape: 16-17 minutes. Firm muffins that hold their shape: 18-20 minutes.

To prevent the muffin liner from sticking, make sure to let the muffins cool completely before taking it off.