Chewy Rye Chocolate Chip Cookies

In this take on classic chocolate chip cookies I use organic rye flour to create these Chewy Rye Chocolate Chip Cookies that are sweet and nutty. Adding rye flour in addition to all purpose flour adds a hearty flavor that makes these cookies perfect for fall baking!

If you like twists on classic chocolate chip cookies, check out Pumpkin Oatmeal Chocolate Chip Cookies, Espresso Walnut Chocolate Chip Cookies, Healthy Chocolate Chip Cookies with Coconut Sugar, or Kamut Flour Chocolate Chip Cookies.

rye chocolate chip cookie with flaky sea salt broke in half on a white marble counter.

A Quick Look At The Recipe

Recipe Name: Chewy Rye Chocolate Chip Cookies
Ready In: 1 hour 30 minutes
Makes: 18 cookies
Main Ingredients: salted butter, light brown sugar, rye flour, chocolate chips
Flavor Profile: nutty flavor, rich chocolate and flaky sea salt in every bite
Dietary Info: no seed oils
Difficulty: Easy!
Why You’ll Love It: chocolate chip cookies with nutty organic rye flour

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Why You'll Love This Recipe

Twist on a Classic: This recipe takes a classic chocolate chip cookie and adds rye flour for additional depth of flavor!
Soft & Chewy: These are soft and chewy cookies with a crispy edge, just like my Eggless Chocolate Chip Cookies.
Sweet & Salty: I love adding flaky sea salt on top of these cookies because it gives them that sweet and salty combo that I am obsessed with! If you love sweet and salty, also check out Brown Butter Caramel Dark Chocolate Cookies.
Hearty Flavor: The rye flour brings a hearty flavor which balances out the sweetness perfectly. If you like a less sweet cookie, you'll love this combo.

Jump to:

A Quick Look At The Recipe
Why You’ll Love This Recipe
Ingredients
Baker’s Tips
How to Make Chewy Rye Chocolate Chip Cookies
Recipe FAQ’s
More Chocolate Chip Cookies
Chewy Rye Chocolate Chip Cookies
The Bake Shop

Rye Chocolate Chip Cookies offer a cozy, bakery-style vibe with a hint of nutty depth from rye flour and pools of melty chocolate chips. They have a tender chewy center with crispy edges—the kind of cookie that tastes even better after it cools and the flavors settle. If you love contrasting textures and a not-too-sweet profile, these belong in your weekly bake rotation alongside Vanilla Sea Salt Chocolate Chip Cookies, Double Chocolate Pumpkin Cookies, Espresso Walnut Chocolate Chip Cookies, or Eggless Chocolate Oatmeal Raisin Cookies.

Make it a little cookie-and-coffee moment by pairing a warm tray of rye cookies with an Iced Blueberry Latte. Or enjoy with a cozy drink like Caramel Hot Cocoa, Healthy Gingerbread Hot Cocoa with Bone Broth, Coconut Hot Chocolate, or Chai Tea Hot Chocolate.

Ingredients

Butter: I use organic salted butter, but unsalted butter is fine if you prefer. Just add 1/4 teaspoon of salt to the recipe. Be sure to check out Best Salted Butter for Baking for my top picks for soft and chewy cookies.
Light Brown Sugar: I'm using my homemade light brown sugar, but store bought also works.
Vanilla Extract: Just be sure to use a high quality vanilla extract, not imitation.
Rye Flour: I use King Arthur Organic Rye Flour, this is my top pick! This is what gives these cookies their amazing hearty flavor.
All Purpose Flour: I also use a mix of organic all purpose flour for the perfect texture.
Leavening: I use baking soda and baking powder to get a perfect texture in these cookies while using the rye flour.
Chocolate Chips: I use organic semi sweet chocolate chips, but dark chocolate chips also works. This chocolate chip cookie recipe is flexible too, so if you want to use a chopped up chocolate bar, milk chocolate even white chocolate you can if that's your preference (though I'm partial to semi sweet and dark chocolate myself!).
Flaky Sea Salt: I top these cookies with flaky sea salt. This part is optional, but if you love sweet and salty cookies as much as I do, then you'll want to do this!

*For a full list of ingredients and measurements, visit the recipe card below.

Baker's Tips

Always use a digital food scale for the best results.
Make sure your butter is soft for the best chocolate chip cookies. I prefer to leave butter out on the counter to soften naturally as that's the best method.
I use all light brown sugar in this recipe for an extra chewy cookie, if you don't have light brown sugar, you can easily make your own with my recipe for Homemade Light Brown Sugar with just two ingredients you probably already have! Using all light brown sugar makes incredibly soft chocolate chip cookies!
It's important to refrigerate the cookie dough, otherwise these can spread too much.
I use flaky sea salt on top, feel free to leave it off if you don't want a salty cookie. Or, you could even use fine sea salt if that's all you have.
High Altitude — Bake at 375°F for 11 to 14 minutes or until lightly browned on the bottoms.

How to Make Chewy Rye Chocolate Chip Cookies

butter and brown sugar in a glass mixing bowl on a white marble counter.

In the bowl of a stand mixer fitted with the paddle attachment, add the butter, light brown sugar, and vanilla extract. Mix on low until combined, then continue to cream butter and sugar for 5 minutes until light and fluffy.

ingredients for rye chocolate chip cookies in a glass mixing bowl on a white marble counter.

Add the eggs, all purpose flour, rye flour, baking powder, baking soda, and sea salt in that order.

rye chocolate chip cookie dough in a glass mixing bowl on a white marble counter.

Mix on low until combined into a dough.

Add the chocolate chips, and mix on low to combine.

rye chocolate chip cookie dough balls on a baking sheet on a white marble counter.

Line a baking sheet with parchment paper. Using your hands, form the dough into 18 balls and place them on the prepared baking sheet. Place the baking sheet in the fridge for 1 hour. Preheat the oven to 375°F. Line another baking sheet with parchment paper. Transfer half the cookies to the second baking sheet, and space them 1-inch apart.

rye chocolate chip cookies with flaky sea salt on a baking sheet.

Bake for 12 to 15 minutes or until lightly browned on the bottoms. Sprinkle with flaky sea salt immediately after they come out of the oven. Allow to cool completely on the baking sheet. (If baking at high altitude, be sure to check the Notes for high altitude baking instructions).

plate of rye chocolate chip cookies with flaky sea salt on a plate on a white marble counter.

Recipe FAQ's

What does rye flour do in cookies?

Rye flour provides a hearty and nutty flavor that just adds depth to a classic chocolate chip cookie. It also gives these cookies a much chewier texture compared to using just all purpose flour. And it pairs really well with the rich chocolate and flaky sea salt in this cookie recipe.

Does rye flour contain gluten?

Yes, rye flour does contain gluten. Even though it has less gluten than traditional wheat, if you're gluten free you still should not eat rye flour.

Does rye flour make cookies denser?

Yes, but in a good way as it makes these cookies chewier since I use it in combination with all purpose flour for a great balance. Rye flour has a heartier texture and it increases tenderness and chewiness because it's more absorbent.

Why does rye pair well with chocolate?

Rye pairs so well with chocolate because there's a great contrast between rye flour's nutty and hearty flavor combined with chocolate's rich, smooth and creaminess that is a match made in heaven.

Can I substitute all-purpose flour for rye flour?

You can, but you'll just have plain chocolate chip cookies. The magic of this recipe lies in the mixture of using rye flour in combination with classic ingredients.

What if I don't have light brown sugar?

You can easily make your own with my recipe Homemade Light Brown Sugar. You could also use half cane sugar and half dark brown sugar in its place which would give you very similar results.

Can I use a cookie scoop?

Yes! The cookie scoop and I do not get along, so I always hand roll. But, you can definitely use a cookie scoop if you prefer.

Why didn’t my cookies spread?

If you didn't measure properly, too much dry ingredients compared to wet ingredients will cause cookies not to spread as the ratios are off. Ensure you are using a digital food scale for accurate measuring every time!

Should cookies be soft when they come out of the oven?

Yes, these cookies will be incredibly soft when they come out of the oven. You need to let them cool completely on the baking sheets before handling or moving.

How should I store rye chocolate chip cookies?

These are soft and chewy cookies so be sure to store them in an airtight container to keep them fresh. They will stay fresh at room temperature for up to a week, but I think they are best within a few days of baking. You can also store them in an airtight container in the freezer for up to 3 months.

stack of rye chocolate chip cookies with sea salt on a plate on a white marble counter with fresh flowers.

More Chocolate Chip Cookies

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