Name: Chewy Fresh Milled Spelt Chocolate Chip Cookies
Prep time: 15 min
Cook time: 12 min
Total time: 147 min
Ingredients: 1 1/2 cups fresh milled spelt flour (approximately 1 cup of spelt berries); 1/2 tsp baking soda; 1/2 tsp unrefined salt; 1 cup organic cane sugar; 1 tbsp molasses (alternatively, use store-bought light brown sugar); 1/2 cup grass-fed butter; 1 whole egg; 2 egg yolks; 1 tsp vanilla extract; 6 oz dark chocolate chips; flaky sea salt for topping (optional)

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These chewy chocolate chip cookies are made with fresh milled spelt flour, and are completely irresistible! They are a healthier alternative to a traditional chocolate chip cookie with nutrients from freshly milled ancient grains.

Fresh baked spelt chocolate chip cookies on a wooden board with spelt grains

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If you are looking to start using fresh milled flour in more recipes, I’ve got you covered! You should definitely try fresh milled flour pancakes, fresh milled cream of wheat, and fresh milled flour muffins next!

Reasons to Love Fresh Milled Spelt Cookies

Fresh Milled Grains – Milling your flour fresh gives these cookies better flavor and nutrition than anything made with store-bought flour.

Perfect Texture – These cookies have the classic chocolate chip cookie texture everyone loves, with a rich, slightly nutty flavor from spelt. They are chewy and dangerously good!

More Nourishing Than Traditional Cookies – Okay hear me out. This is still a dessert, but using whole grain spelt flour adds fiber, protein, and minerals you don’t get from refined white flour. And while you probably aren’t eating cookies for the nutrition, it’s a great added bonus!

Ancient Grains – Spelt is an ancient grain that many people find easier to digest than modern wheat. It is believed that spelt was first used about 8,000 years ago, making it one of the oldest crops in human history (source).

Real-Food Ingredients – like all my favorite recipes on this blog, these spelt cookies use simple ingredients you can feel good about baking with and feeding your family.

Great Introduction to Fresh Milled Baking – If you’re new to milling your own flour, this recipe is an easy place to start because it doesn’t require yeast or any rise time. Just mix up the cookies, refrigerate then bake!

Close up shot of fresh milled spelt chocolate chip cookies on a cooling rack

Benefits of Freshly Milled Flour

Using flour right after it’s been milled from the wheat berry has so many benefits. Once grains are milled, important nutrients like vitamins, healthy fats, and antioxidants begin to degrade within 24 hours, which is why store-bought flour is almost always enriched (putting the vitamins and nutrients back in). The problem with enriching flour is that these nutrients are synthetic and much harder for your body to absorb and use. Milling your flour fresh and using it within 24 hours preserves naturally occurring B vitamins, vitamin E, iron, magnesium, and fiber, and the flavor of fresh flour is hard to beat! Baking with fresh milled flour allows you to use ancient grains like spelt in their most nutrient dense form, giving you an end result that is delicious and more satisfying.

Spelt flour specifically is has higher contents of copper, iron, zinc, magnesium and phosphorus than wheat flour (source). In terms of flour, spelt is also decently high in protein. One cup of spelt flour has about 10 grams.

Ingredients in Fresh Milled Spelt Chocolate Chip Cookies

Spelt berries or fresh milled spelt flour – For the best nutrition, mill the spelt yourself or use it within 24 hours of milling.

Grass-fed butter – I always prefer to use grass-fed butter for the best quality and nutrition. I use salted butter in all my recipes because it’s what I buy and always have in my fridge. I like the kerrygold irish butter.

Unrefined sea salt – My favorite is always redmonds real salt

Organic cane sugar + molasses – I love to make my own brown sugar for this recipe, which might seem extra but I love the depth of flavor it adds to these spelt chocolate chip cookies. You can also just use regular light brown sugar if you prefer!

Egg + egg yolks – eggs are another ingredient that can really vary in quality and nutrition. Pasture raised eggs are always the best way to go.

Vanilla extract and baking soda

Dark chocolate chips – I like to buy 60/70% dark chocolate chips. You can get really good ones from Azure standard, or just use your favorite from your local grocery store.

optional – flaky sea salt for after baking (highly highly recommend!!)

Bowl of spelt grain next to spelt chocolate chip cookies on a countertop

Other supplies you might need

grain mill – a must have if you want to mill your own spelt. I have been loving my mockmill 100
stand mixer, electric mixer, or plain old bowl & spoon will do the trick
small saucepan
medium bowl
plastic wrap
baking sheet
unbleached parchment paper
measuring cups and spoons

How To Make Chocolate Chip Spelt Cookies

Step 1: Mill your spelt berries (if using spelt flour then skip this step)

Step 2: Combine flour, baking soda, and salt in a medium mixing bowl.

Step 3: Melt butter in a small saucepan over medium-low heat.

Step 4: While the butter melts, mix your brown sugar by combining sugar and molasses together with a spoon until all of the clumps are gone and the sugar becomes light and fluffy just like brown sugar. If you are using store-bought brown sugar, skip this step.

Hand mixing molasses into cane sugar to make brown sugar

Step 5: In the bowl of your stand mixer (or if mixing by hand, a medium bowl) combine the melted butter and brown sugar using a paddle attachment. Add the egg and egg yolks and mix together. Add the vanilla extract.

Step 6: Slowly add the dry ingredients to the wet ingredients and mix until just combined.

Step 7: Gently fold in the chocolate chips

Step 8: Cover your bowl with plastic wrap or a tea towel and place in the fridge for at least 2-3 hours.

Step 9: When you are ready to bake cookies, preheat the oven to 375 degrees.

Step 10: Line a baking sheet or cookie sheet with unbleached parchment paper, and roll the cookie dough into small balls, 3 ish tbsp in size. You can also use a cookie scoop for even proportioning. The cookies will spread as they bake, so make sure to space 3″ apart.

Step 11: Bake the cookies for 10-12 minutes, or until they are just turning golden brown. Be careful not to over bake! Baking time may vary depending on your oven, so experiment until you get the time down.

Fresh baked spelt flour chocolate chip cookies with flaky sea salt

Step 12: When you remove the cookies from the oven, gently tap the baking sheet to deflate the cookies slightly. Sprinkle with flaky sea salt.

Step 13: Repeat the process with the remaining cookie dough.

Step 14: Let the cookies cool, and enjoy!

Vertical image of fresh baked spelt flour chocolate chip cookies and flaky sea salt

Storage & Make-Ahead Tips For Spelt Cookies

How to store spelt chocolate chip cookies
Cool the cookies completely on a wire rack, and then store them in an airtight container at room temperature for up to 3 days. For longer storage, I like to put them in a zip lock bag in the freezer. They are honestly super good right from the freezer, they don’t even have to thaw first!

Freezing baked cookies:
Like i mentioned, these cookies freeze really well. Cool the cookies completely and put them in a freezer-safe container or zip lock bag and freeze them for up to 3 months. Thaw at room temperature or eat them straight from the freezer (pro tip)

Freezing cookie dough:
If you want to make cookie dough ahead of time for quick grab and bake cookies, measure the dough into balls and flash freeze them on a baking sheet. Once they are frozen, you can move the balls of dough to a freezer bag. You can bake them straight from the freezer, just add an extra 1-2 minutes onto your total bake time.

Make-ahead option:
You can mix the dough up to 24 hours in advance and refrigerate it until you are ready to bake.

Troubleshooting Tips for Fresh Milled Spelt

My cookies spread a lot. What happened?
Spelt has a more delicate gluten structure than most modern wheat varieties. Make sure you chill the dough for 2-3 hours before baking to help reduce the spreading. Keep in mind that these cookies are not as “fluffy” as some chocolate chip cookies that use regular flour.

The dough feels very soft or sticky. Is that normal?
Yes — fresh milled spelt flour absorbs liquid differently and often creates a softer dough. Avoid adding too much extra flour, which can dry out the cookies. Enough chill time in the fridge before baking helps the dough to harden a bit.

My cookies are crumbly.
This usually means the dough is too dry or you might have cooked them too long. Measure flour carefully and remove cookies from the oven when the edges are set and turning brown but the centers are still soft.

They didn’t rise much.
Spelt cookies won’t puff like refined flour cookies. This is normal and the texture we are going for.

Can I overmix spelt dough?
Yes. Overmixing can weaken spelt’s fragile gluten structure, leading to crumbly cookies. Mix just until combined.

Why do fresh milled cookies taste better the next day?
Fresh milled flour continues to hydrate after baking, improving texture and flavor as the cookies rest.

Blue plate filled with fresh milled spelt chocolate chip cookies next to a bowl of spelt grain

Where To Buy Spelt

You may be able to find spelt berries at your local health food store, or I like to buy mine at Azure Standard. You can buy them in bulk for a really reasonable price, and they will keep for a long time if stored correctly.

Frequently Asked Questions

Spelt is an ancient wheat variety with a slightly nutty, mildly sweet flavor. It’s less processed than modern wheat and often easier to digest for some people.

You can, but the result will be completely different. I would suggest following a different recipe if you prefer not to use spelt flour.

Fresh milled flour gives the best flavor and nutrition, but you can use store-bought whole spelt flour if needed.

Yes chilling the dough is recommended! Chilling the dough for 2-3 hours can help the cookies hold their shape when baked.

Absolutely. Cookie dough balls freeze well for up to 3 months, and baked cookies can be frozen once fully cooled.

Store baked cookies in an airtight container at room temperature for up to 3 days, or freeze to keep them fresh for longer.

They’re still cookies, but using fresh milled spelt flour adds whole grain fiber, minerals, and nutrients you don’t get from refined flour.