Chocolate Einkorn Protein Muffins are perfect for a quick breakfast or easy snack. These moist, fluffy muffins are filled with delicious flavor and extra protein. Pair them with a large glass of milk for a match made in heaven!

A stack of einkorn protein muffins on a cooling rack on a white counter with a white tea towel

We have early mornings here at the farmhouse. And there is no shortage of chores to be done. 

Some days, I don’t have as much time as I’d like to make a nice warm breakfast for everyone. So, I have been loving having some muffins on hand as an easy alternative. They are great to make the night before and enjoy easily the next morning. 

Now, your average muffin does not contain a lot of protein. As I was trying to come up with ways to make sure we were starting our day off right, I had the idea to add collagen peptides to the muffins for a little protein boost.

After a few trials, I finally ended up with the perfect moist muffin. (Check out my roundup of my favorite muffin recipes here.) 

These muffins are a great alternative to regular muffins, especially if you are having a hard time getting in protein in you or your child’s diet. 

Chocolate einkorn protein muffins Pinterest photo

Why you’ll love this recipe:

Extra protein – Thanks to the collagen peptides, yogurt, and einkorn flour, these muffins boast a higher protein content than your average muffins. Yet, they are still moist and delicious! It is a great way to sneak in some more nutrients for picky eaters and to help balance blood sugars. Keep you feeling fuller long without as much of a crash.

An easy breakfast or snack – Muffins are a perfect on-the-go snack or meal. Plus, this is a super easy recipe! All you have to do is mix the ingredients and bake. Nothing complicated about it!

Chocolatey and delicious – I love how chocolaty these are! They taste rich and decadent. You’d never know they were full of healthy ingredients!

Tips 

  • I’ve used date sugar in replace of granulated sugar, and it worked great! 
  • I typically end up with enough dough to get 15 muffins. Instead of dirtying another muffin tin for those extra 3, I usually bake the first 12, and then the remaining batter after. I don’t like to wash more than one muffin tin if I don’t need to. 
  • You can also make a double batch of these and freeze to have on hand for a quick snack. 
An einkorn protein muffin with the liner off to show texture and other muffins in background on cooling rack on a white counter top
Want to save this recipe?
Just enter your email and get it sent to your inbox! Plus you’ll get new recipes from us every week!
Please enable JavaScript in your browser to complete this form.

FAQ

Does einkorn flour have high protein?

Einkorn flour is an ancient grain and is known for being higher in protein than other flours. It’s also a good source of B vitamins and iron. (Dr. Axe)

Can einkorn replace all-purpose flour?

Einkorn can replace all-purpose flour, but not always one-for-one. Usually, recipes will need to be adjusted. This is due to the high protein content in einkorn and its varying gluten structure. For einkorn specific recipes, check out some of mine here

Is einkorn the healthiest flour?

Einkorn is typically considered healthier than its modern wheat counterparts. When processed, there is less nutrient loss. This is great due to the fact it is full of things such as protein, fiber, B vitamins, iron, and even antioxidants. Thanks to its nutrients, it carries health benefits such as easing allergies, assisting in weight loss, and more. (Dr. Axe)

Although einkorn is NOT gluten free, it does tend to be easier to digest. This is because instead of strong, stretchy gluten, it is made up of weaker, brittle gluten that breaks up easier. (Jovial Foods)

This post contains affiliate links, which means I make a small commission at no extra cost to you. See my full disclosure here.

Tools you may need

Muffin pans or tins

Muffin liners

Large mixing bowl

Small bowl

Wooden spoon

Measuring cups and spoons

a chocolate einkorn protein muffin cut in half showing the inside texture with other muffins in the background on a white counter top

Ingredients 

All purpose einkorn flour – You can sub fresh ground einkorn flour as well. I’ve even done half and half with success. 

Granulated sugar – I’ve also made this with date sugar, and it turned out great! You could also experiment with coconut sugar as well for more natural sweetener alternatives. 

Baking soda

Collagen – I get my collagen from Thrive Market, but you should also be able to find it at your local grocery store or health food store. Costco also has collagen peptides for a really great price (extra bonus if you get it on sale).

Cocoa powder

Salt – I like to use good sea salt. 

Chocolate chips

Eggs

Plain yogurt – I use homemade yogurt from the milk we get from our cows. See how to make your own yogurt in the instant pot here

Oil – I’ve used avocado oil, coconut oil, and butter. All work great! 

Milk

Vanilla Extract – Store bought or homemade works. Learn how to make homemade vanilla here

einkorn protein muffins lined up on a cooling rack on a white counter top

How to make Einkorn Protein Muffins

Preheat your oven to 375 degree F. Add liners to a muffin tins.

Mix ingredients together

four images showing a woman making einkorn protein muffins

In a large bowl, mix the all purpose einkorn flour, sugar, baking soda, collagen, cocoa powder, and salt together. 

In a separate bowl, mix the eggs, plain yogurt, oil, milk and vanilla.

Add the wet ingredients to the dry ingredients mixture, along with the chocolate chips. Mix until well incorporated, but don’t over mix! 

Add batter to muffin tin

four images showing a woman mixing the final ingredients for einkorn protein muffins and adding to muffin tin and baking

Fill each liner in the muffin tin with batter. I use a measuring cup to fill it almost to the top. 

I usually get 15 muffins out of this recipe. So, I’ll make the first 12 and then make the remaining muffins next. 

Bake

Bake for 15 – 20 minutes until a toothpick comes out clean. 

Enjoy! The best way to enjoy (at least for us here at the farmhouse) is fresh out of the oven with a cold glass of milk!

einkorn protein muffins stacked on top of each other on a white counter top with a white tea towel in background

How to store

Store the muffins in an airtight container on the counter for a couple of days or in the fridge for longer storage. You can also freeze these muffins for up to 3 months.

More breakfast and snack ideas 

If you try this recipe and love it, I would love if you could come back and give it 5 stars! Tag me on Instagram @farmhouseonboone.

Chocolate Einkorn Protein Muffins

4.82 from 43 votes
Chocolate Einkorn Protein Muffins are perfect for a quick breakfast or easy snack. These moist, fluffy muffins are filled with delicious flavor and packed with protein.
Prep: 15 minutes
Cook: 20 minutes
Total: 35 minutes
Servings: 15
An einkorn protein muffin with the liner off to show texture and other muffins in background on cooling rack on a white counter top
Save this recipe!
Just enter your email and get it sent to your inbox! Plus you’ll get new recipes from us every week!
Please enable JavaScript in your browser to complete this form.

Ingredients 

  • 2 cups all purpose einkorn flour
  • 3/4 cup granulated sugar, I’ve also tried date sugar and it worked great
  • 1 teaspoon baking soda
  • 1/3 cup collagen peptides
  • 1/2 cup cocoa powder
  • 1/2 teaspoon salt
  • 1 1/2 cups chocolate chips
  • 2 large eggs
  • 3/4 cup plain yogurt, 185g
  • 1/2 cup oil, 120ml
  • 1/2 cup milk, 120ml
  • 1 teaspoon vanilla

Instructions 

  • Add liners to a muffin tin and preheat your oven to 375 degree F. 
  • In a large bowl, mix the all purpose einkorn flour, sugar, baking soda, collagen, cocoa powder, and salt together. 
  • In a separate bowl, mix the eggs, plain yogurt, oil, milk and vanilla.
  • Add the wet ingredients to the dry ingredients mixture, along with the chocolate chips. Mix until well incorporated, but don't over mix! 
  • Fill each liner in the muffin tin with batter. I use a measuring cup to fill it almost to the top. 
  • I usually get 15 muffins out of this recipe. So, I’ll make the first 12 and then make the rest next. 
  • Bake for 15 – 20 minutes until a toothpick comes out clean. 

Notes

  • I typically end up with enough dough to get 15 muffins. Instead of dirtying another muffin tin for those extra 3, I usually bake the first 12, and then the remaining batter after. I don’t like to wash more than one muffin tin if I don’t need to.

Nutrition

Calories: 303kcal | Carbohydrates: 37g | Protein: 9g | Fat: 14g | Saturated Fat: 5g | Polyunsaturated Fat: 2g | Monounsaturated Fat: 5g | Trans Fat: 0.03g | Cholesterol: 27mg | Sodium: 186mg | Potassium: 154mg | Fiber: 2g | Sugar: 21g | Vitamin A: 61IU | Vitamin C: 0.1mg | Calcium: 48mg | Iron: 1mg

Nutrition information is automatically calculated, so should only be used as an approximation.

Like this? Leave a comment below!

Sharing is caring!

4.82 from 43 votes (36 ratings without comment)

Leave a comment

Your email address will not be published. Required fields are marked *

Recipe Rating




64 Comments

  1. Samuel Pihlaja says:

    An interesting discussion might be priced at comment I do think that you need to write read more about this topic, it might be described as a taboo subject but typically consumers are not enough to communicate on such topics To another location Cheers

  2. Becky Dunn says:

    Coul I use normal flour? And can these be loger fermented

    1. Becky Dunn says:

      Sorry, auto fill!
      Could I use normal flour and long ferment these?
      We cannot get einkorn in NZ

  3. Kayla says:

    5 stars
    I have made this recipe probably 20 times and it has become my kids absolute favorite! It makes this mommas heart happy to know my kids are getting a good amount protein while also eating something they love.

  4. Beth says:

    5 stars
    These were delicious! Super moist and yummy. I made these into mini muffins and only baked them for about 12 minutes and they came out great!

  5. Donna Cox says:

    5 stars
    I made these this morning, and they were delicious! They tasted like brownie bites! I’ll definitely make them again! Thank you for sharing this recipe!

  6. Kimberly says:

    This is an amazing recipe, thank you for sharing! I am curious if a substitution could be made and swap peanut butter for the chocolate portions of the recipe? I am not a chocolate fan but really need easy0 ways of incorporating more protein into my diet.

    1. Lisa Bass says:

      Sure thing!

      1. Jolene says:

        Have you ever tried adding zucchini? If no, any guess what I might need to balance it out with if I do add it?

        1. Lisa Bass says:

          You could do that!

  7. Adrien says:

    5 stars
    This recipe remains a HUGE hit in my house, and my kids request it every week. I love your channel and blog and only just started experimenting with Einkorn this year. I trust your recipes and especially loved that this one snuck in some extra protein. Easy ingredients for anyone with a real food pantry and fridge, but I’ve also used sour cream in lieu of yogurt when I was out, which also worked great. I always go for the date sugar, with no complaints from the kiddos. Thanks for all of your amazing recipes and resources! As a working mom, real food meals can be a struggle. Easy, pre-vetted recipes like these are a God-send!

  8. Leigh Anne says:

    These turned out dry. Could it be because I used almost half Greek yogurt as I didn’t have enough plain yogurt? Should I have added more milk to them?

    1. Lisa Bass says:

      That could have been the reason since Greek yogurt is so much thicker than regular. I would’ve added just enough milk to the greek yogurt to give it the consistency of regular yogurt.

  9. Rebecca Egan says:

    I’m wondering how I could make these discard protein muffins instead. We love all your recipes!!

    1. Lisa Bass says:

      You can add the discard to them. Here’s a blog post about turning any recipe into a sourdough recipe. In this case, you’d still keep the baking powder because you’re adding discard instead of active starter.

  10. cheryl vallerie says:

    What if you want to omit the collagen peptides?

    1. Lisa Bass says:

      You can. It shouldn’t effect the recipe too much.