Last Updated on September 28, 2026 by Michelle

Fresh milled einkorn chocolate chip cookies have changed my life.

I’ve always been a chocolate chip cookie snob. But back in the day, that meant following the Nestle Tollhouse recipe to a T, including using refined, bleached all-purpose flour, refined white sugar, margarine sticks for “butter,” and Nestle chips.

Let’s just say, things have changed a little.

Fresh milled einkorn chocolate chip cookies

My chocolate chip cookies these days involve:

fresh milled, whole grain, ancient einkorn flour (learn all about einkorn here)
unrefined sugar (coconut sugar) and organic cane sugar
real butter (feel free to brown your butter for even more flavor, like I do in this recipe for Kamut Chocolate Chip Cookies)
chocolate chips made with coconut sugar (linked below)

…And my chocolate chip cookies have never tasted better. Toll house has nothing on my fresh milled einkorn chocolate chip cookies.

What is einkorn?

Depending on who you ask, einkorn is often considered the oldest grain that still exists today.

Einkorn is an ultra nutritious ancient grain. (source) Unlike modern grains that are hybridized for specific traits that increase productivity (and wind up weakening nutrients), einkorn still has the simple genetic makeup that it had in ancient times.

Einkorn, like other ancient and heritage grains, offers us more carotenoids and phenolic compounds than is found in modern wheat. (source)

Can I use store bought einkorn flour in chocolate chip cookies?

If you don’t have a grain mill, or don’t want to mill your own flour, you can use this einkorn fresh flour.

Another great option if you need a substitute for the einkorn flour in this recipe? This stoneground barley flour.

Although milling your own flour is always best, both of these flours from organic farmers as as close to milling your own as you can get.

What is fresh milled flour?

We all know that flour comes from wheat.

But what lots of folks don’t realize is that the flour they buy at the store is hardly even the same product as the wheat it started out as. Commercial flour has been heated, treated, and sifted until it’s left with just one out of the three parts of a wheat berry.

Commercial flour is just starch, when it should be starch + bran + germ = whole grain flour.

Add on top of that, most flour contains at least 3 additional preservatives, enzymes or dough conditioners, plus synthetic vitamins (made in a lab instead of nature).

Milling your own flour allows you to turn wholegrain wheat berries into the freshest flour in the world. Your body will thank you.

Learn how to mill your own flour here.

What do I need to make fresh milled einkorn chocolate chip cookies?

First, you need a grain mill and einkorn wheat berries. Other than that, these cookies are made with pretty standard ingredients you should have on hand:

butter
coconut sugar (or sub brown sugar)
organic cane sugar
vanilla extract
eggs
fresh milled einkorn flour
fresh milled chickpea flour or you could use cornstarch (optional, gives a chewier texture)
baking powder
chocolate chips

Grab my free pantry checklist with details and discounts on all my favorite ingredients.

Where should I buy einkorn flour/einkorn wheat berries?

Unfortunately, there are lots of “knockoffs” in the ancient grain world.

Lower-quality grains trying to pass for high-quality ancient grains. I only trust one of my favorite regenerative wheat farmers when I stock up on einkorn wheat berries.

You can check local natural food stores for wholegrain einkorn berries, or purchase from bulk food suppliers like Azure Standard.

If you don’t have a grain mill or don’t want to mill your own flour, you can purchase stoneground, organic einkorn flour (as close to milling your own as you can get!) from one of my favorite regenerative wheat farmers here. Another great option is to substitute barley for einkorn in these cookies. Another favorite small, organic family farm offers fresh milled barley flour.

Tips for baking with einkorn flour

Einkorn has a naturally sweet, buttery flavor, so you might find that you actually add less sugar to anything you make with einkorn.

As with all fresh milled flour, einkorn flour can sometimes hydrate differently than all-purpose flour would. Add flour to all recipes slowly, and don’t be afraid to add more/less einkorn flour than a recipe calls for in order to get to a proper consistency.

If you’re milling your own einkorn flour to make a somewhat “delicate” recipe, consider cooling your freshly milled einkorn flour before using it, so your butter doesn’t warm up too much when mixed with the flour. (This is especially helpful with pie crusts and biscuits; you can stick the flour in the fridge or freezer to cool down before using.)

Go here for everything you want to know about this amazing ancient grain: Einkorn 101: history, milling, flaking, cooking & more

Fresh milled einkorn chocolate chip cookies recipe

INGREDIENTS for einkorn chocolate chip cookies

3/4 cup butter at room temperature

1/2 cup coconut sugar (or brown sugar)

1/2 cup organic cane sugar

1 tsp vanilla extract

2 eggs

2 cups fresh milled einkorn flour (220 grams)

1 cup fresh milled hard red flour (130 grams)–see notes for my favorite

3 tsp baking powder

1 tsp chickpea flour (fine and sifted)–see notes

1 cup chocolate chips

DIRECTIONS for einkorn chocolate chip cookies

Cut up butter into 1-tablespoon-size chunks and mix them with the sugars on medium speed, just until well mixed (over mixing may heat up your butter too much and make your fresh flour cookies too thin).
Add in vanilla and eggs, just until mixed.
Mix einkorn and hard red flours, baking powder, and chickpea flour together and add to mixer until everything is combined.
Mix in chocolate chips and form balls (I make our cookie size about 40 grams each). Dough is often a little crumbly, but this results in a nice chewy, soft cookie in the end, so simply press the dough and chips together with your hands to form balls. Place cookie balls on cookie trays about 2 inches apart and flatten each cookie ball with the bottom of a glass or a cookie press.
Bake in oven at 350 for 7 minutes, removing tray from oven but letting cookies rest on hot trays until they are almost cool. Move to cooking rack until fully cooled then store in air-tight container.

NOTES for einkorn chocolate chip cookies

I only order my einkorn grains from this family farm, that I know I can trust to raise organic, regeneratively grown wheat. They’re also always clean grains, stored well. (Or you can try the flour here.)
This is my favorite hard red wheat for this recipe. (Or you can try the flour here.) I try to use organic, heritage grains when I’m able to, over modern, hybrid grains, which aren’t as nutrient-dense.
I mill chickpea flour instead of using refined cornstarch (see how here), using these organic chickpeas (also called “garbanzo beans”) in my Mockmill Lino 200 (find my mill here), but you can skip this ingredient (it just helps your cookies be a little chewier).

Try a Test Cookie

If this is your first time making this cookie recipe, you may want to do a few test cookies before baking the whole batch, because fresh flour behaves differently in different kitchens and different conditions. If so, hold back about 1/2 cup (55 grams) of the einkorn flour in step 3 and form a single test cookie before step 4 (adding in some chips by hand to the test cookie). Bake the test cookie and let it cool to see if it is the consistency you want. If it is too thin, add in half of the reserved einkorn flour to your mixing bowl, mix well, and make another test cookie. Do this until you have a cookie you are pleased with, then move on to step 4 and bake your entire batch.

Print Recipe

fresh milled einkorn chocolate chip cookies

soft, chewy chocolate chip cookies made with ancient grain einkorn flour

Keyword: ancient grain, chocolate chip cookies, einkorn, fresh milled flour

Servings: 2 dozen

Equipment

grain mill

Ingredients

3/4 cup butter at room temperature
1/2 cup coconut sugar or brown sugar
1/2 cup organic cane sugar
1 tsp vanilla extract
2 eggs
2 cups fresh milled einkorn flour 220 grams
1 cup fresh milled hard red flour 130 grams
3 tsp baking powder
1 tsp chickpea flour fine and sifted
1 cup chocolate chips

Instructions

Cut up butter into 1-tablespoon-size chunks and mix them with the sugars on medium speed, just until well mixed (over mixing may heat up your butter too much and make your fresh flour cookies too thin).
Add in vanilla and eggs, just until mixed.
Mix einkorn and hard red flours, baking powder, and chickpea flour together and add to mixer until everything is combined.
Mix in chocolate chips and form balls (I make our cookie size about 40 grams each). Dough is often a little crumbly, but this results in a nice chewy, soft cookie in the end, so simply press the dough and chips together with your hands to form balls. Place cookie balls on cookie trays about 2 inches apart and flatten each cookie ball with the bottom of a glass or a cookie press.
Bake in oven at 350 for 7 minutes, removing tray from oven but letting cookies rest on hot trays until they are almost cool. Move to cooking rack until fully cooled then store in air-tight container.