Einkorn Chocolate Chip Cookies (Chewy, Gooey + Freezer-Friendly)

These einkorn chocolate chip cookies have the perfect crispy edges, a soft gooey center, and a subtle nutty flavor from the ancient grain flour — and I have lost count of how many times I’ve brought a batch somewhere and had everyone ask me for the recipe.

They freeze so well, which means you can have a warm homemade cookie ready in minutes without touching a mixing bowl.

Why These Are the Best Einkorn Chocolate Chip Cookies

I’ve made a lot of batches of these cookies. I’ve brought them to school events, dinner parties, holiday gatherings — and every single time without exception, someone pulls me aside and asks what I put in them. There is something about the texture and flavor that people can’t quite place but can’t stop eating.

The secret is the einkorn flour. It bakes differently than regular all-purpose flour in the best possible way. The cookies come out with a slightly deeper, nuttier flavor that makes a standard chocolate chip cookie taste almost one-dimensional by comparison. The texture is what really gets people — crispy golden edges that give way to a soft, gooey center that stays that way even the next day.

Two things make this recipe specifically stand out from other einkorn cookie recipes. First, the ingredient list uses things you can actually find — organic butter, brown sugar, organic cane sugar, eggs, vanilla, baking soda, salt, and chocolate chips. No specialty sweeteners that require a separate trip to a health food store. Just a better version of a classic cookie.

Second: the smoosh technique. This is my trick for getting that perfectly thick, gooey center that doesn’t spread flat, and I’ll walk you through exactly how to do it below.

And because this is Healthier Homemade — they freeze perfectly. Make a double batch, freeze the dough balls, and pull out exactly as many as you need whenever you need them. My kids think I bake fresh cookies all the time. I do not.

What Is Einkorn Flour?

If you haven’t baked with einkorn before, here’s what you need to know. Einkorn is one of the oldest cultivated grains in the world — an ancient wheat that has never been hybridized or genetically modified the way modern wheat has been. It’s been grown essentially the same way for thousands of years.

What that means practically for baking is a few things. Einkorn has a different gluten structure than modern wheat — it’s a weaker gluten, which makes doughs slightly stickier and more delicate. It also means that many people who find modern wheat hard to digest tolerate einkorn much better. It is not gluten-free, so it is not safe for anyone with celiac disease.

Flavor-wise, einkorn has a natural nuttiness and slight sweetness that you simply don’t get from conventional all-purpose flour. In cookies especially, it adds something that makes people say “what IS that flavor?” — in a good way.

For this recipe, use all-purpose einkorn flour (not whole wheat einkorn). Jovial Foods is the most widely available brand and what I recommend. You can find it at most health food stores, Whole Foods, or online.

Key Ingredient Notes

All-purpose einkorn flour. This is not interchangeable 1:1 with regular flour without adjustments — see the substitution section below if you need to swap. Use Jovial Foods all-purpose einkorn for the most consistent results. If you’re using freshly milled einkorn berries, see the fresh-milled notes in the FAQ.

Organic butter. Use real, unsalted butter. Melt it fully before mixing — melted butter (rather than softened) is what gives these cookies their chewy, dense center rather than a cakey texture. Make sure it has cooled slightly before adding the eggs so you don’t scramble them.

Brown sugar + organic cane sugar. The combination of both is key. Brown sugar adds moisture and a caramel depth that keeps the cookies chewy. The granulated sugar helps the edges crisp up. Don’t substitute all of one for the other or the texture changes. Organic evaporated cane sugar and regular organic granulated sugar are the same thing for the purposes of this recipe — use whichever you have.

Eggs at room temperature. Room temperature eggs incorporate more evenly into the butter and sugar mixture. Take them out of the fridge 30 minutes before you start, or place them in a bowl of warm water for 5 minutes if you forgot.

Vanilla extract. Use real vanilla extract, not imitation. Two teaspoons sounds like a lot — it’s not. Einkorn has a strong enough flavor that it needs a generous amount of vanilla to balance it.

Chocolate chips. We like Real Good or Nestlé Simply brands — clean ingredient lists and they melt beautifully. Use whatever you love. Semi-sweet is the classic choice but dark chocolate chips are excellent with the nuttiness of the einkorn.

Variations and Substitutions

Regular flour swap. If you don’t have einkorn flour, use ¾ cup of regular all-purpose flour for every 1 cup of einkorn flour called for. The cookies will still be delicious — the nutty flavor won’t be there, but the texture will be similar.

Dark chocolate chips. A great swap if you want more bittersweet flavor to contrast the slightly sweet einkorn. Dark chocolate and einkorn are a really good combination.

Add sea salt on top. A pinch of flaky sea salt pressed on top of each cookie right before baking takes these from great to unforgettable. Highly recommended.

Add nuts. Chopped walnuts or pecans folded in with the chocolate chips add a great crunch and lean into the nutty einkorn flavor even more.

Dairy-free. Swap the butter for a good quality plant-based butter. The texture will be slightly different but the cookies still come out well.

Coconut sugar. You can substitute coconut sugar 1:1 for the granulated cane sugar. The cookies will be slightly darker and have a more caramel-forward flavor.

How to Make Einkorn Chocolate Chip Cookies

1. Preheat the oven to 350°F and line two baking sheets with parchment paper.
2. Whisk the dry ingredients. In a small bowl, whisk together the 2¾ cups all-purpose einkorn flour, 1 tsp baking soda, and 1 tsp pink Himalayan salt. Set aside.
3. Mix the wet ingredients. In a large bowl, combine the 1 cup melted organic butter, ¾ cup organic brown sugar, ¾ cup organic cane sugar, and 2 tsp vanilla extract. Mix until combined and slightly fluffy — about 60–90 seconds with a hand mixer or stand mixer on medium.
4. Add the eggs. Beat in the 2 large room-temperature eggs one at a time until fully incorporated.
5. Add the dry ingredients. Gradually add the flour mixture to the wet ingredients, stirring until just combined. Do not overmix — stop as soon as you no longer see dry streaks of flour. Overmixing einkorn dough develops the gluten too much and can affect texture.
6. Fold in the chocolate chips. Add the 1 cup chocolate chips and stir by hand until evenly distributed.
7. Scoop and chill. Using a 2-tablespoon cookie scoop, portion the dough onto the parchment-lined baking sheets, spacing at least 2 inches apart. Refrigerate the entire baking sheet for at least 30 minutes. Don’t skip this step — chilling the dough is what keeps the cookies thick and prevents them from spreading flat. The einkorn flour needs time to fully absorb the moisture in the dough.
8. Bake for 10–12 minutes. Bake until the edges are just golden brown. The centers will look slightly underdone and soft — that’s exactly right. They will set up as they cool.
9. Do the smoosh immediately. See below — this step happens right when the cookies come out of the oven.
10. Cool on the baking sheet. Let the cookies rest on the hot baking sheet for 3–5 minutes before transferring to a wire rack. This finishing time on the hot pan continues cooking the centers slightly without overbaking them.

The Smoosh Technique

This is my signature move and the reason these cookies have that perfect thick, gooey center instead of going flat.

The moment the cookies come out of the oven — immediately, while they’re still very hot and soft — use two forks to gently push the sides of each cookie inward toward the center. You’re essentially smooshing the edges in toward the middle. It takes about 2 seconds per cookie.

What this does: hot cookies fresh from the oven are still pliable. By pushing the edges in, you create a slightly thicker center and more defined edges. As the cookie cools and sets, it holds that shape. The result is a cookie that looks bakery-thick with a gooey, soft center — not the flat, crispy-all-the-way-through version you get when you skip it.

Work fast. Once the cookies cool even slightly, they set and the technique won’t work. Have your forks ready the moment the oven timer goes off.

How to Freeze the Dough (and Baked Cookies)

This is one of the reasons I make a double batch every single time.

Freezing the dough balls: After scooping the dough, place the portions on a parchment-lined baking sheet and freeze until solid — about 1–2 hours. Transfer the frozen dough balls to a freezer-safe Ziploc bag and freeze for up to 3 months. Label with the date and baking instructions. When you’re ready to bake, place the frozen dough balls on a lined baking sheet and let them sit at room temperature for 15–20 minutes, then bake at 350°F for 12–14 minutes (a couple of minutes longer than fresh since they’re starting cold).

Freezing baked cookies: Let the baked cookies cool completely, then freeze in a single layer on a sheet pan until solid. Transfer to a freezer bag for up to 3 months. To thaw, set on the counter for 20–30 minutes or microwave for 15–20 seconds for a warm, just-baked texture.

The frozen baked cookie trick is one of my favorites for busy weeks — my kids come home from school and think I’ve been baking all day. I have not. Future you will be very glad you made a double batch today.

Expert Tips

Chill the dough — no shortcuts. Thirty minutes is the minimum. Longer is better. You can even make the dough the night before and refrigerate it overnight. Chilling does two things: it prevents spreading and it gives the einkorn flour time to fully absorb the moisture, which improves the final texture significantly.

Don’t overmix after adding the flour. Einkorn has a more delicate gluten structure than modern wheat. Overmixing develops the gluten too much and can make the cookies tough. Mix only until you no longer see dry streaks.

Melt and cool the butter. Fully melted butter (not just softened) gives these cookies their chewy, dense texture. But let it cool for 5–10 minutes before adding it to the sugar — hot butter can start cooking the eggs.

Do the smoosh the moment they come out. See the section above. Have your forks ready. This step only works on hot cookies.

Underbake slightly. Pull the cookies when the edges are just golden and the centers still look soft. They continue cooking on the hot pan. Waiting for them to look fully done in the oven means they’ll be overdone by the time they cool.

Use a cookie scoop. A 2-tablespoon cookie scoop gives you evenly sized cookies that bake at the same rate. Uneven portions mean some are overdone before others are ready.

A note on measuring einkorn flour. Einkorn flour packs differently than regular flour and a packed cup can throw off the whole recipe. Spoon the flour lightly into your measuring cup and level it off — don’t scoop directly from the bag. If you have a kitchen scale, 330 grams is the right amount for this recipe and takes all the guesswork out of it.

Expert Tips

Chill the dough — no shortcuts. Thirty minutes is the minimum. Longer is better. You can even make the dough the night before and refrigerate it overnight. Chilling does two things: it prevents spreading and it gives the einkorn flour time to fully absorb the moisture, which improves the final texture significantly.

Don’t overmix after adding the flour. Einkorn has a more delicate gluten structure than modern wheat. Overmixing develops the gluten too much and can make the cookies tough. Mix only until you no longer see dry streaks.

Melt and cool the butter. Fully melted butter (not just softened) gives these cookies their chewy, dense texture. But let it cool for 5–10 minutes before adding it to the sugar — hot butter can start cooking the eggs.

Do the smoosh the moment they come out. See the section above. Have your forks ready. This step only works on hot cookies.

Underbake slightly. Pull the cookies when the edges are just golden and the centers still look soft. They continue cooking on the hot pan. Waiting for them to look fully done in the oven means they’ll be overdone by the time they cool.

Use a cookie scoop. A 2-tablespoon cookie scoop gives you evenly sized cookies that bake at the same rate. Uneven portions mean some are overdone before others are ready.

A note on measuring einkorn flour. Einkorn flour packs differently than regular flour and a packed cup can throw off the whole recipe. Spoon the flour lightly into your measuring cup and level it off — don’t scoop directly from the bag. If you have a kitchen scale, 330 grams is the right amount for this recipe and takes all the guesswork out of it.

Frequently Asked Questions

What is einkorn flour and where do I buy it? Einkorn is an ancient wheat that has been grown essentially unchanged for thousands of years. Unlike modern wheat, it has never been hybridized or modified, which gives it a different gluten structure and a naturally nuttier, sweeter flavor. It’s easier to digest for many people who are sensitive to modern wheat, though it is not gluten-free. Jovial Foods is the most widely available brand — you can find it at Whole Foods, many health food stores, or online.

Can I use regular flour instead of einkorn? Yes. Use ¾ cup of regular all-purpose flour for every 1 cup of einkorn flour in this recipe. The cookies will still be delicious but won’t have the same nutty depth of flavor.

Can I use freshly milled einkorn flour? Yes, with adjustments. Freshly milled einkorn flour has more moisture than store-bought all-purpose einkorn, which means you’ll need slightly less of it. Reduce the flour by ¼ to ⅛ cup per cup called for in the recipe, and add 1–2 tablespoons of water to compensate. The dough texture will guide you — it should be scoopable but not runny.

What is evaporated cane sugar — can I use regular sugar? Yes. Evaporated cane sugar and organic granulated cane sugar are essentially the same thing for baking purposes. Evaporated cane sugar is slightly less refined but the consistency and measurement are identical. Use whichever you have.

Why did my cookies come out flat? Two most common causes: the dough wasn’t chilled long enough, or the flour was slightly under-measured (a packed cup of einkorn can lead to too little flour). Make sure to chill for at least 30 minutes and spoon the flour lightly into the measuring cup rather than scooping. Alternatively, add 2–3 extra tablespoons of flour if the dough feels very loose after mixing.

Why are my cookies dry or cakey? Usually too much flour. Einkorn packs very easily in a measuring cup, so it’s easy to accidentally add more than the recipe calls for. Use the spoon-and-level method or weigh the flour (330 grams for this recipe).

How do I store these cookies? At room temperature in an airtight container for up to 4 days. Freeze baked cookies for up to 3 months — see the freezing section above for full instructions.

Are einkorn chocolate chip cookies healthier than regular cookies? They’re made with an ancient grain that many people find easier to digest and that has a higher nutrient density than modern wheat — more protein, more antioxidants, and a different gluten structure. They still have butter and sugar, so they’re a treat. But they’re a better version of a treat, which is exactly what Healthier Homemade is about.

You Might Also Like These Recipes:

S’mores Cookies (Einkorn Flour + Clean Ingredients)

White Chocolate and Strawberry Cookies

Print Recipe

5 from 1 vote

Best Gooey Einkorn Chocolate Chip Cookies

Einkorn chocolate chip cookies with crispy golden edges, a soft gooey center, and a rich nutty flavor from ancient grain flour. Chilled dough and the smoosh technique are the secrets to getting the perfect texture every time. Freezer-friendly — make a batch now and pull from frozen whenever you need a warm cookie fast.

Prep Time15 minutes mins

Cook Time9 minutes mins

Total Time25 minutes mins

Course: Dessert, Snack

Cuisine: American

Keyword: best cookie recipe, best cookies, chocolate chip, chocolate chip cookies, einkorn chocolate chip cookies

Servings: 24

Calories: 110kcal

Equipment

• 2 baking sheets
• 2 bowls
• 1 mixer or beater

Ingredients

• 2 ¾ cup all-purpose einkorn flour
• 1 tsp baking soda
• 1 tsp pink Himalayan salt
• 1 cup organic butter
• ¾ cup organic brown sugar
• ¾ cup organic cane sugar
• 2 tsp organic vanilla extract
• 2 large egg (room temperature)
• 1 cup chocolate chips (real good or nestle simple)

Get Recipe Ingredients

Instructions

• Preheat your oven to 350°F (175°C). Line 2 cookie sheets with parchment paper.
• In a small bowl, whisk together the dry ingredients of 2 ¾ cup all-purpose einkorn flour,1 tsp baking soda, and 1 tsp pink Himalayan salt
• In a separate large bowl combine your wet ingredients- cream together the 1 cup organic butter melted,¾ cup organic brown sugar, ¾ cup organic cane sugar, and2 tsp organic vanilla extract. Mix until light and fluffy.
• Beat in the 2 large egg until well combined.
• Gradually add the dry ingredients to the wet mixture, stirring until just combined.
• Fold in the 1 cup chocolate chips until evenly distributed throughout the dough.
• Using a 2 tbsp cookie scoop, scoop the dough onto the prepared baking sheet lined with parchment paper, spacing them at least 2 inches apart.
• Refrigerate for at least 30 minutes.
• Bake for around 10-12 minutes, or until the edges are golden brown.
• Remove from the oven and immediately use the smoosh technique. Smoosh the sides in towards each other slightly with 2 forks.
• Let the cookies cool on the baking sheet for a few minutes before transferring them to a wire rack to cool completely.

Notes

Don't skip the chill. Refrigerate the scooped dough for at least 30 minutes before baking. This prevents spreading and gives the einkorn flour time to absorb moisture. Overnight chilling works great too.

The smoosh technique. The moment cookies come out of the oven, use two forks to gently push the sides inward toward the center. This creates a thick, gooey center and holds its shape as the cookie cools. Work fast — it only works while they're very hot.

Measuring flour. Spoon the einkorn flour lightly into the measuring cup and level it off. Do not scoop directly from the bag or the cookies may come out dry. For best results, weigh the flour: 330 grams.

Regular flour swap. Use ¾ cup regular all-purpose flour for every 1 cup einkorn flour.

Fresh-milled einkorn. Reduce flour by ¼ cup and add 1–2 tablespoons of water to account for the higher moisture content of freshly milled flour.

Freeze the dough balls for up to 3 months. Bake from frozen at 350°F for 12–14 minutes.

 

 

 

 

 

 

 

 

 

Nutrition

Serving: 1cookie | Calories: 110kcal | Carbohydrates: 14g | Protein: 1g | Fat: 5g | Saturated Fat: 3g | Cholesterol: 18mg | Sodium: 125mg | Fiber: 0.5g | Sugar: 9g

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