It tastes like chocolate cake, but it has zucchini in it so it’s healthy, right? Seriously, these muffins are so tasty. They are light, fluffy, and super moist (thanks to that zucchini)! Chocolate einkorn zucchini muffins are a must for a breakfast treat.
Why Bake with Einkorn?
Aren’t All Grains “Ancient”?
Einkorn is an ancient grain. If you’re like my husband, you just said to yourself all grains are ancients. Well, yes and no. Traditional grains have changed over the years and many have been genetically modified to increase yields. This sounds great from a business perspective, but it is not so great for your gut.

So the “ancient grains” that you will hear about in the health community are grains that have remained largely unchanged over the course of the last several centuries. Some you may have heard of are:
- Spelt
- Kamut
- Emmer
- Einkorn
However, there are more grains outside of the wheat family that are also considered ancients grains which you can read about over on the Whole Grains Council website.

What Is Einkorn? And Why Should I Use It To Make Chocolate Zucchini Muffins?
Einkorn is a type of wheat that has never been hybridized and only has two sets of chromosomes. It has significantly less gluten proteins making it easier to digest for those with gluten sensitivity. Einkorn is also higher in protein and lower in carbohydrates than modern wheat.

Those benefits alone were a game-changer for me. I had to forgo all wheat products due to gluten sensitivity in middle school. Baking with einkorn and sourdough as an adult has allowed me to bring so many delicious treats back into my diet.
Since then I have been experimenting with einkorn recipes and these chocolate einkorn zucchini muffins are one of my new favorites!
How to Shred Zucchini
Zucchini is super simple to shred. If you use a cheese grater, you can use the average-sized whole or the small holes to change the texture of your baked good. I suggest using the smaller holes for this recipe.
Or if you have a KitchenAid mixer, use the shredder attachment! When I have zucchini coming out of my ears from the garden in the summer that is my preferred method of shredding.
Can I Use Frozen Zucchini?
Yes! I use frozen shredded zucchini from my summer garden for this recipe all the time. Just thaw it out the day before, remove as much excess water as possible, and you are good to go!



When using thawed zucchini, use the measurement amount from when you froze it, not from when you thawed it out and removed the excess water. While the amount of zucchini you have did not change, its volume will likely appear much less until you mix it into the batter.
Ingredients for Chocolate Einkorn Zucchini Muffins
6 tablespoons of melted unsalted butter
1/2 cup of honey
1/2 cup of plain whole-milk yogurt
2 eggs
1 tsp of pure vanilla extract
2 cups of finely shredded zucchini – squeezed to remove excess water.
1 1/2 cups of einkorn flour – all-purpose or whole wheat (I make mine with freshly ground whole wheat einkorn flour)
1/2 cup of cocoa powder
1 teaspoon of baking powder
1 teaspoon of baking soda
1/2 teaspoon of salt
1 teaspoon of ground cinnamon
1/2 cup of semi-sweet chocolate chips (optional but delicious)

How to Make Chocolate Einkorn Zucchini Muffins
Preheat the oven to 350 degrees Fahrenheit.
Line a 12 cup muffin tin with muffins cups.
In a glass measuring cup melt 6 tablespoons of unsalted butter.
Add a 1/2 cup of honey to the measuring cup.
Pour the honey and butter into a mixing bowl.
Add a 1/2 cup of whole-milk yogurt, 2 eggs, and 1 teaspoon of vanilla extract to the bowl and mix on medium speed until completely combined.
Next, add your dry ingredients to the mixing bowl:
- 1 1/2 cups of einkorn flour
- 1/2 cup of cocoa powder
- 1 tsp of baking powder
- 1 tsp of baking soda
- 1/2 tsp of salt
- 1 tsp of ground cinnamon

With the mixer on low, combine the dry ingredients into the wet ingredients.
Remove the excess water from the shredded zucchini by either squeezing it in a tea towel or in a zip lock bag. I use frozen shredded zucchini from my garden. For this recipe, I allow it to thaw in the fridge and then squeeze as much of the water out as possible from its bag before adding it to the batter.
Remove the mixing bowl from the mixer and fold in the zucchini and semi-sweet chocolate chips using a spatula.
Spoon the chocolate einkorn zucchini muffin batter into the prepared muffin tin. You can bake any excess batter in a small oven-safe glass dish.
Bake for 18-21 minutes.
Allow the muffins to cool for 10 minutes before transferring them from the tin to a cooling rack.
Chocolate Einkorn Zucchini Muffins

Ingredients
- 6 tbsp melted unsalted butter
- 1/2 cup of honey
- 1/2 cup of whole-milk plain yogurt
- 2 eggs
- 1 tsp of vanilla extract
- 2 cups of shredded zucchini
- 1 1/2 cups of einkorn flour (whole wheat or all-purpose)
- 1/2 cup of cocoa powder
- 1 tsp of baking powder
- 1 tsp of baking soda
- 1/2 tsp of salt
- 1 tsp of ground cinnamon
- 1/2 cup of semi-sweet chocolate chips
Instructions
- Preheat the oven to 350 degrees Fahrenheit.
- Line a 12 cup muffin tin with muffins cups.
- In a glass measuring cup melt 6 tablespoons of unsalted butter.
- Add a 1/2 cup of honey to the measuring cup.
- Pour the honey and butter into a mixing bowl.
- Add a 1/2 cup of whole-milk yogurt, 2 eggs, and 1 teaspoon of vanilla extract to the bowl and mix on medium speed until completely combined.
- Next, add your dry ingredients to the mixing bowl: 1 1/2 cups of einkorn flour, 1/2 cup of cocoa powder, 1 tsp of baking powder, 1 tsp of baking soda, 1/2 tsp of salt, 1 tsp of ground cinnamon.
- With the mixer on low, combine the dry ingredients into the wet ingredients.
- Remove the excess water from the shredded zucchini by either squeezing it in a tea towel or in a zip lock bag. I use frozen shredded zucchini from my garden. For this recipe, I allow it to thaw in the fridge and then squeeze as much of the water out as possible from its bag before adding it to the batter.
- Remove the mixing bowl from the mixer and fold in the zucchini and semi-sweet chocolate chips using a spatula.
- Spoon the batter into the prepared muffin tin. You can bake any excess batter in a small oven-safe glass dish.
- Bake for 18-21 minutes.
- Allow the muffins to cool for 10 minutes before transferring them from the tin to a cooling rack.
Notes
Whole-grain einkorn tends to soak up less moisture. Therefore, if your batter seems a bit runny because you had a juicy zucchini, simply add more flour.
Enjoy!
Other Breakfast Recipes You Might Enjoy:
- The Best Einkorn Banana Bread
- Quick and Easy Flaky Sourdough Biscuits
- How to Make Crispy Breakfast Potatoes
- Sourdough Dutch Baby
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