Mimi's Organic Eats » Recipes » Cookies » Rye Chocolate Chip Cookies
Rye Chocolate Chip Cookies
Cookies • No Seed Oils • High Altitude • Fall Recipes | Published September 7, 2022 by Mimi Council
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In this take on classic chocolate chip cookies I use King Arthur Organic Rye Flour to create these 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 my Pumpkin Oatmeal Chocolate Chip Cookies, Coconut Chocolate Chip Cookies, or my Kamut Flour Chocolate Chip Cookies.

Table of Contents
These Rye Chocolate Chip Cookies taste sweet, salty, and hearty with the addition of the rye flour. They are the best chocolate chip cookies with rye flour. And I think they are the perfect chocolate chip cookie for fall. Crispy on the edges and soft in the middle, just like your favorite soft chocolate chip cookies! These Rye Chocolate Chip Cookies have more depth of flavor, bringing a sophistication to classic soft chocolate chip cookies.
These are the best chocolate chip cookies for fall. They will just make you just say that's a really good chocolate chip cookie. With the perfect balance of sweet, hearty, and salty (thanks to the addition of flaky sea salt on top), I hope you'll try out these Rye Chocolate Chip Cookies! These are one of my new favorite chocolate chip cookie recipes, and they will be made often in my house.


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, just like a classic chocolate chip.
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!

Ingredients
- Butter: I use Organic Valley Salted Butter.
- Light Brown Sugar: I'm using my homemade light brown sugar recipe, but store bought also works.
- Vanilla Extract: My favorite is Simply Organic. Just be sure to use a high quality vanilla extract, not imitation.
- Eggs: Use large eggs.
- 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.
- Salt: Use a fine sea salt.
- Chocolate Chips: I use organic semi sweet chocolate chips, but dark chocolate also works.
- 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!

Tools Needed
- Scale: Always use a digital food scale for the best results.
- Stand Mixer: I use my stand mixer for ease, but you can also use a hand mixer if you prefer.
- Baking Sheets: You'll need two half sheet pans to bake the cookies.
- Parchment Paper: I always use nontoxic parchment paper for ease, cleanup, and I think it bakes the best cookies.
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Step by Step Instructions
Step 1
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.
Step 2
Add the eggs, all purpose flour, rye flour, baking powder, baking soda, and sea salt in that order and mix on low until combined into a dough. Add the chocolate chips, and mix on low to combine.



Step 3
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.
Step 4
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.



Step 5
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).

Baker's Tips
- 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, if you don't have light brown sugar, you can easily make your own with my recipe for How to Make 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.
FAQ's
You can easily make your own with my recipe How to Make Light Brown Sugar. You could also use half cane sugar and half dark brown sugar in its place.
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.
These are soft and chewy cookies so be sure to store them in an airtight container to keep them fresh.

Craving More?
- 12 Best Flours to Bake With
- Kamut Flour Chocolate Chip Cookies
- Brown Sugar Shortbreads
- Malted Chocolate Chip Cookies
- Eggless Chocolate Chocolate Chip Cookies

Rye Chocolate Chip Cookies
Mimi CouncilIngredients
- 113 grams salted butter (softened)
- 226 grams light brown sugar (packed)
- 2 teaspoons vanilla extract
- 2 large eggs
- 165 grams all purpose flour
- 90 grams rye flour
- ½ teaspoon baking powder
- ½ teaspoon baking soda
- ½ teaspoon fine sea salt
- 198 grams semi sweet chocolate chips
- Flaky sea salt
Instructions
- 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.
- Add the eggs, all purpose flour, rye flour, baking powder, baking soda, and sea salt in that order and mix on low until combined into a dough. Add the chocolate chips, and mix on low to combine.
- 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.
- 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.
- Store in an airtight container for up to 7 days.
Notes
Nutrition
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The rye flour adds so much flavor to these chocolate chip cookies!