The Best Einkorn Zucchini Chocolate Chip Muffins with Fresh-Milled Flour
Soft, tender, and full of garden-fresh zucchini and melty chocolate chips, these Fresh-Milled Einkorn Zucchini Chocolate Chip Muffins are an easy way to use up summer zucchini. Made with freshly milled einkorn wheat, warm cinnamon, vanilla, and plenty of chocolate chips, they make a delicious breakfast, snack, or after-school treat.
There are some recipes that just taste like summer.
Fresh zucchini from the garden. A warm kitchen. The smell of something sweet baking in the oven. And, of course, chocolate chips—because zucchini may make these muffins moist, but chocolate chips make everyone actually excited to eat them.
These zucchini chocolate chip muffins are made with freshly milled einkorn wheat, giving them a tender texture and the naturally nutty, slightly sweet flavor that makes einkorn such a wonderful grain for muffins and quick breads.
And if your garden has entered its annual “How on earth did we grow this much zucchini?” phase, you’re going to want this recipe.
Why You’ll Love These Einkorn Zucchini Muffins
- Made with freshly milled einkorn flour
- A great way to use fresh garden zucchini
- Soft and tender without being overly sweet
- Loaded with chocolate chips
- Easy enough for a weekday breakfast
- Perfect for lunchboxes and after-school snacks
- Can easily be baked as a zucchini chocolate chip loaf
- Freezer-friendly
Why Bake With Fresh-Milled Einkorn?
Einkorn is one of my favorite grains to use in sweet breads, muffins, and quick breads.
When you mill einkorn fresh, you’re using the entire wheat berry rather than a flour that has had portions of the grain removed during processing. Freshly milled einkorn also has a wonderful flavor—slightly nutty, naturally sweet, and almost buttery.
Because einkorn behaves differently from modern wheat, it is important not to treat the batter like a traditional wheat muffin batter.
Don’t overmix it.
Once the flour is added, stir just until everything is combined. Einkorn can become sticky and gummy when overworked, and nobody wants a zucchini muffin with a gummy center.
The Secret to Great Zucchini Muffins
Zucchini contains a LOT of water.
That moisture is wonderful for making tender muffins, but too much water can leave you with a soggy or gummy center.
For this recipe, shred the zucchini and give it a light squeeze before adding it to the batter. You don’t need to wring it completely dry. We want some of that natural moisture—just not all of it.
If your zucchini is particularly large and watery, you may need to squeeze it a little more.
Ingredients
Fresh-Milled Einkorn Flour
For the best flavor and texture, mill your einkorn berries fresh immediately before making the muffins.
Zucchini
Freshly shredded zucchini provides moisture and tenderness.
Eggs
Eggs help bind the muffins and provide structure.
Oil
A neutral oil keeps these muffins wonderfully moist. You can also use melted butter if you prefer a richer flavor.
Sugar
A little brown sugar adds sweetness and a subtle caramel flavor that pairs beautifully with einkorn and chocolate.
Vanilla and Cinnamon
These two ingredients make the muffins taste warm and bakery-style without needing a lot of extra sugar.
Chocolate Chips
Because zucchini muffins are better with chocolate.
I like using semi-sweet chocolate chips, but milk chocolate or dark chocolate work beautifully too.
Soft Fresh Milled Einkorn Zucchini Chocolate Chip Muffins
Yield: 12 muffins
Prep time: 15 minutes
Bake time: 18–22 minutes
Oven temperature: 350°F
Ingredients
1 ¾ cups freshly milled einkorn flour, about 180 grams
1 teaspoon baking soda
½ teaspoon baking powder
½ teaspoon salt
1 teaspoon cinnamon
2 large eggs
½ cup brown sugar, packed
½ cup neutral oil or melted butter
2 teaspoons vanilla extract
1 ½ cups finely shredded zucchini, lightly squeezed
¾ cup chocolate chips
Instructions
- Preheat the oven to 350°F. Line a 12-cup muffin pan with paper liners or grease the pan well.
- Mill your einkorn wheat. Measure approximately 180 grams of einkorn berries and mill them on a fine setting.
- In a medium bowl, whisk together the freshly milled einkorn flour, baking soda, baking powder, salt, and cinnamon.
- In a separate large bowl, whisk together the eggs, brown sugar, oil or melted butter, and vanilla.
- Add the shredded zucchini to the wet ingredients and stir to combine.
- Add the dry ingredients to the wet ingredients. Stir gently just until the flour is incorporated. Do not overmix.
- Fold in the chocolate chips, reserving a few to sprinkle over the tops if desired.
- Divide the batter evenly between the 12 muffin cups. They should be approximately ¾ full.
- Sprinkle a few additional chocolate chips over the tops.
- Bake at 350°F for 18–22 minutes, or until the tops spring back lightly when touched and a toothpick inserted into the center comes out with a few moist crumbs.
- Allow the muffins to cool in the pan for about 5 minutes before transferring them to a cooling rack.
How Do I Know When Zucchini Muffins Are Done?
Because zucchini adds so much moisture, don’t rely solely on the color of the muffins.
The best way to tell is to check the center with a thermometer.
I like to pull these muffins when the center reaches approximately 200–205°F.
They will continue to cook slightly as they cool and set.
You can also use the traditional toothpick test. The toothpick should come out with a few moist crumbs but should not have wet batter clinging to it.
Fresh-Milled Einkorn Baking Tips
Don’t overmix the batter.
This is especially important with einkorn. Stir gently and stop as soon as the flour disappears.
Don’t completely dry out your zucchini.
A little moisture is exactly what makes these muffins soft and tender. Just squeeze out enough excess liquid that the zucchini isn’t dripping wet.
Let the batter rest briefly if needed.
Fresh-milled flour can continue absorbing liquid as it sits. If your batter looks unusually loose, give it a few minutes before adding anything else.
Don’t overbake.
The muffins will continue setting as they cool. Overbaking will give you a much drier muffin.
Use fresh-milled einkorn for the best flavor.
Einkorn has a naturally rich, nutty flavor that pairs especially well with cinnamon, vanilla, zucchini, and chocolate.
How to Turn These Into an Einkorn Zucchini Chocolate Chip Loaf
Don’t have time to make individual muffins?
Turn the exact same batter into a beautiful zucchini chocolate chip quick bread.
Grease an 8½ x 4½-inch loaf pan and pour the prepared batter into the pan.
Bake at 350°F for approximately 45–55 minutes.
Begin checking the loaf around 45 minutes. The top should be golden brown and the center should be set.
For the most accurate result, check the center with an instant-read thermometer. You’re looking for approximately 200–205°F in the center.
If the top begins browning too quickly before the center is finished, loosely tent the loaf with foil for the remainder of the baking time.
Allow the loaf to cool in the pan for about 10–15 minutes before removing it to a cooling rack.
For especially clean slices, let the loaf cool completely before cutting.
Can I Make Mini Loaves?
Absolutely!
Divide the batter between 3–4 mini loaf pans, depending on their size.
Bake at 350°F and begin checking them around 25–30 minutes. Baking time will vary depending on the size and depth of your pans.
Can I Freeze Einkorn Zucchini Muffins?
Yes!
Allow the muffins to cool completely. Place them in a freezer-safe container or bag and freeze for up to approximately 3 months.
To serve, thaw at room temperature or warm briefly in the microwave.
You can also freeze the zucchini loaf. I recommend wrapping it tightly before placing it in a freezer bag.
Frequently Asked Questions
Can I use regular whole wheat flour instead of einkorn?
Yes. The recipe was developed for freshly milled einkorn, so the texture will change somewhat if you substitute another grain. If using another freshly milled wheat, you may need to make a small adjustment to the liquid depending on the grain.
Do I have to peel the zucchini?
No! There is no need to peel zucchini before shredding it.
Should I squeeze the zucchini?
Yes, but only lightly. Remove excess dripping moisture while leaving enough moisture behind to keep the muffins tender.
Can I use frozen zucchini?
Yes. Thaw it completely and squeeze out excess moisture before measuring and adding it to the batter.
Can I leave out the chocolate chips?
Of course—but around here, that would probably be considered a questionable decision.
You can also substitute chopped chocolate, dark chocolate chips, or mini chocolate chips.
Why are my einkorn muffins gummy?
The most common reasons are too much moisture, overmixing, or underbaking. Make sure excess liquid is removed from the zucchini, stir the batter gently, and bake until the center is fully set.
A Little Zucchini, a Little Einkorn, and a Lot of Chocolate
This is exactly the kind of recipe I love keeping around during zucchini season.
It’s simple enough to make on a weekday morning, special enough to serve to company, and practical enough to turn an overflowing basket of zucchini into something everyone will happily eat.
And when the muffins disappear, you can make the loaf.
Because when the garden gives you zucchini, you might as well make chocolate chip muffins.
Recipe at a Glance
Fresh-Milled Einkorn Zucchini Chocolate Chip Muffins
Freshly milled einkorn flour combines with garden zucchini, cinnamon, vanilla, and chocolate chips to make soft, tender muffins that are perfect for breakfast, snacks, and lunchboxes.
Prep: 15 minutes
Bake: 18–22 minutes
Yield: 12 muffins
Temperature: 350°F
Loaf option: Bake the same batter in an 8½ x 4½-inch loaf pan at 350°F for approximately 45–55 minutes.
Storage
Store completely cooled muffins in an airtight container at room temperature for up to 3 days.
For longer storage, freeze the muffins for up to 3 months.
Fresh Milled Einkorn Chocolate Chip Zucchini Muffins
Ingredients
Wheat Berries for Freshly Milled Flour
- 210 g about 1¾ cups whole einkorn berries
Wet Ingredients
- 120 g ½ cup plain Greek yogurt
- 125 g ⅓ cup honey
- 2 large eggs
- 55 g ¼ cup avocado oil or melted coconut oil
- 2 teaspoons vanilla extract
Dry Ingredients
- 1 teaspoon baking soda
- ½ teaspoon baking powder
- ½ teaspoon fine sea salt
- ½ teaspoon cinnamon
- ⅛ tsp allspice
Mix-Ins
- 175 g about 1½ cups finely shredded zucchini, lightly squeezed
- 140 g 3/4 cup mini dark chocolate chips, reserving 2-3 Tablespoons for topping the muffins
Instructions
- Mill the Einkorn. Measure 210 g (about 1¾ cups) einkorn wheat berries. Mill the einkorn berries on a fine setting and set aside.
- Prepare the Zucchini. Finely shred the zucchini in food processor. Place it in a clean kitchen towel and gently squeeze out some of the excess moisture. Do not wring the zucchini completely dry. The remaining moisture is important for creating soft, tender muffins. Measure 175 g (about 1½ cups) after lightly squeezing.
- Combine the Dry Ingredients. In a medium bowl, whisk together the freshly milled einkorn flour, baking soda, baking powder, fine sea salt, and cinnamon. Set aside.
- Combine the Wet Ingredients. In a large mixing bowl, whisk together the Greek yogurt, honey, eggs, avocado oil, and vanilla until smooth.
- Make the Batter. Add the dry ingredients to the wet ingredients. Using a spatula, gently fold the mixture together just until the flour is incorporated.
- Do not overmix. Einkorn has a delicate gluten structure, and gentle mixing helps keep these muffins tender.
- Rest the Batter. Let the batter rest for 10 minutes. This allows the freshly milled einkorn to absorb the moisture and helps create a more cohesive, tender crumb. After resting, the batter should be thick and scoopable. If it seems unusually stiff, gently stir in 1–2 tablespoons of milk.
- Preheat the oven to 425°F.
- Add Min-Ins. Stir in the prepared zucchini. Fold in the dark chocolate chips, reserving about 2 1/2 Tablespoons for the tops.
- Fill the Muffin Pan. Line a 12-cup muffin pan with paper liners or lightly grease the cups. Divide the batter evenly between the 12 muffin cups, filling each about 5/8 full. Press a few additional chocolate chips into the tops.
- Bake the Muffins. Bake at 425°F for 5 minutes. Without opening the oven, reduce the temperature to 350°F and continue baking for 13–17 minutes, or until the tops are set and a toothpick inserted into the center comes out with a few moist crumbs.
- Be careful not to overbake. Einkorn muffins are best when they remain soft and moist in the center.
- Allow the muffins to cool in the pan for 5 minutes, then transfer to a wire rack.
- Serve. These muffins are delicious slightly warm while the chocolate chips are still soft, but the flavor and texture are even better once they have cooled completely.
