hand picking up rye chooclate chip cookie from a tray

About These Rye Chocolate Chip Cookies

These chocolate chip cookies are crisp on the edges, and incredibly chewy and flavorful in their middles thanks to a secret ingredient: rye flour! Rye flour, in addition to having a unique nutty whole grain flavor, absorbs 10 times as much water as all-purpose flour. You can learn more in this America’s Test Kitchen article about baking with rye flour.

Using rye flour in chocolate chip cookies makes them extra chewy, and helps keep the cookies fresher for longer.

The best part? The dough comes together quickly and easily with just a bowl and a spatula—no need to bring any ingredients to room temperature, or use a stand mixer! That being said, you will need to rest the dough overnight in the fridge before baking. This makes the cookies extra chewy and flavorful!

Be sure to check out my chocolate chip cookie recipe collection on Hummingbird High, including more unique chocolate chip cookie recipes like these Tender, Chewy & Craggy Chocolate Chip Cookies With Powdered Sugar and Earl Grey Chocolate Chip Cookies.

rye chocolate chip cookies on white parchment paper

Ingredients and Substitutions

Here’s everything you need to make these super chewy and nutty rye chocolate chip cookies:

Shopping List For Rye Chocolate Chip Cookies

And let’s talk about some key ingredients, where to find them, and any potential substitutions:

Common Ingredient Substitutions and Sources

Ingredient FAQ

What are chocolate fèves? Are they the same thing as chocolate baking discs and wafers?

Chocolate fèves are a fancy pastry school term for a flat, bean-shaped disc of chocolate. When baked in a cookie recipe, the fèves don’t hold their shape (similar to how chocolate chips typically do) and instead melt into puddles. These puddles give your cookies thin layers of chocolate throughout every bite. The most prominent maker of chocolate fèves is one of my favorite chocolate makers, Valrhona Chocolate. 

Learn more in my post about The Best Chocolate For Chocolate Chip Cookies.

rye chocolate chip cookies on gold baking tray with an offset spatula

How To Make The Recipe

Here are the basic steps to make these rye chocolate chip cookies from scratch:

  1. Prep the ingredients. (Prep Time: 5 minutes)

  2. Make the cookie dough. (Work Time: 5 minutes)

  3. Prep the cookie dough for baking. (Work Time: 5 minutes)

  4. Chill the cookie dough in the refrigerator overnight. (Chill Time: Overnight)

  5. Thaw the cookies slightly while you preheat the oven. (Prep Time: 10 minutes)

  6. Bake the cookies. (Bake Time: 10 minutes)

Chilling the cookie dough overnight makes these rye chocolate chip cookies extra flavorful and chewy. In fact, there’s bona fide science on it—check out this Serious Eats article talking about how resting cookie dough helps improve its flavor!

In a pinch, you can skip chilling the cookie dough—the cookies will turn out just fine. But they’ll really be special if you take the time to rest the dough!

Additionally, these chocolate chip cookies become chewier after an overnight rest. How? Earlier, I mentioned that rye absorbs 10 times more water and liquid than all-purpose flour. Giving rye flour time to absorb the water from other ingredients like butter and eggs will make the cookies chewier.

process shot showing how to make rye chocolate chip cookies showing unbaked cookie dough in glass bowl
Here’s what the cookie dough looks like after it’s been mixed together.
process shot showing how to make rye chocolate chip cookies scooping cookie dough balls on sheet pan
The fastest and easiest way to make picture-perfect cookies is to invest in a cookie dough scoop—I use a 3-Tablespoon cookie dough scoop.
process shot on how to arrange rye chocolate chip cookies on sheet pan for baking
Here’s what the cookie dough looks like before baking—note the hopscotch spacing of the cookie dough. This allows each portion to melt into the perfect cookie with plenty of space between each one!
Norpro Stainless Steel Scoop 3TBSP

Norpro 3-Tablespoon (50MM) Stainless Steel Cookie Scoop

The fastest and easiest way to make picture-perfect cookies is to invest in a cookie dough scoop. These handy tools scoop the dough into dough balls that bake into perfect cookie circles every time. 
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Recipe Troubleshooting and FAQ

FAQ: Troubleshooting Unexpected Results

Help! My rye chocolate chip cookies came out too puffy. They didn’t sink after baking and don’t look flat like yours. What did I do wrong?

Okay, there are several things that could be responsible for overly puffy cookies:

You didn’t measure the ingredients properly.

If you used cup measures as opposed to weight measures, there’s a larger chance your cookies will come out puffy. 

There’s a LOT of variation in how people use measuring cups. Somebody who scoops ingredients into a measuring cup and packs it down as they go will have a cup that has way more ingredients than somebody who simply scoops the flour into a cup and levels it off as its filled. This is why bakers love measuring by weight with a digital scale instead—it’s much more reliable and completely eliminates any inconsistencies!

Escali Primo Digital Scale

Escali Primo Digital Food Scale

A digital kitchen scale can save you a ton of time and cleanup when baking. A good scale—like this Escali Primo Digital Scale—offers readings in ounces and grams.
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While these variations aren’t a big deal for many recipes, they can be a big deal for cookies. Specifically: if you pack a heavy cup of flour, your cookies will come out too puffy. They won’t fall and sink in the same way as mine did.

So to fill a measuring cup properly, you need to first set the measuring cup on a flat, level surface like your kitchen counter. Spoon the ingredient into the measuring cup until it forms a small mound within the cup. Use a butter knife or bench scraper to level off the mound so that the ingredient is flush with the top edges of the measuring cup.

Finally, if you’re measuring a dry ingredient that has a tendency to clump or get packed down (like flour, confectioners’ sugar, or cocoa powder), give it a quick whisk in its container first. Then, scoop the ingredient into the measuring cup as I described.

You deliberately (or accidentally!) reduced the sugar in the recipe.

Many people often deliberately reduce the sugar in baking recipes for health reasons, or for fear of the recipe being “too sweet.” But the fact is that sugar is in baking recipes for reasons beyond flavor and sweetness! In baking, sugar helps baked good spread evenly and consistently. It also adds moisture and color to the baked goods. If you went this route, it’s likely that your cookies will stay puffy and taste drier than mine.

But how do you accidentally reduce the sugar in the recipe? Similar to how you accidentally use too much flour in a recipe—by failing to use measuring cups and spoons properly. Read my instructions in the question above on how to scoop and fill a measuring cup the right way.

In the FAQ section below, I give you options to freeze your cookie dough for baking later. However, note that you’ll need to thaw the cookie dough slightly when baking from frozen.

What does that mean? Simply set the cookie dough out on a lined sheet pan (the same one you’re planning on baking the cookies on!) as the oven preheats. It usually takes about 10 to 15 minutes for most ovens to preheat. The 10 to 15 minutes out at room temperature will allow the cookie dough to thaw slightly and bake up nicely in the oven. If you skip this thaw, your cookies will come out puffy!

FAQ: Storing The Rye Chocolate Chip Cookies

How To Store Rye Chocolate Chip Cookies

After baking, the cookies can be stored in an airtight container or zip-top bag at room temperature for up to 3 days.

Can you freeze the cookies?

Yes! You can freeze the cookies in the following ways:

  1. Freeze the UNBAKED chocolate chip cookie dough.
    Follow the recipe instructions to make the cookie dough and scoop them out into cookie dough balls. Place the cookie dough balls in a small sheet pan. Cover the pan with plastic wrap and freeze for at least 1 hour, or until the cookie dough balls are frozen solid. Transfer the cookie dough balls to a zip-top bag and freeze for up to 1 year.

    To bake the frozen cookie dough balls, line sheet pans with parchment paper and position the cookie dough balls at least 3 inches apart on the sheet pans. Then, follow the recipe instructions to preheat the oven. Bake for 12 minutes, or until the edges have set but the centers are still gooey.

  2. Freeze the BAKED chocolate chip cookies.
    Individually wrap any leftover chocolate chip cookies in two layers of plastic wrap, then a layer of aluminum foil. The aluminum foil will prevent the cookies from absorbing any other flavors or odors in the freezer. When ready to serve, transfer to the refrigerator to chill overnight. Rewarm in the microwave or in the oven at 350°F for 5 minutes before serving.

Best Recipe Tips

Technique Tips

  • To save myself some clean up, I melt the butter in the bowl I’m planning to make the cookie dough in. Specifically: I use a small bowl to mix the dry ingredients. Then, I use the microwave to melt the butter in a medium bowl big enough to mix the dough in, add the sugars, egg, and extract, then the dry ingredients and chocolate. As a result, I only need two bowls for this recipe!

  • When prepping ingredients, I also melt the butter first. That way, it has time to cool while I prep the rest of the ingredients. Doing so ensures your butter isn’t too hot and won’t scramble the egg when you add it to the dough!

  • Be mindful when melting the butter for these cookies! You don’t want the butter to sizzle, crackle, or pop. I like to chop it up into 1-inch cubes then melt it in a small sauce pot over medium-low heat. Be sure to stir the butter constantly as it melts to help prevent it from overheating.

Troubleshooting Tip

  • If your dough seems too soft to scoop, don’t panic! It’s likely that the butter was still too hot when you combined it with the rest of the ingredients. Simply pop the bowl of cookie dough in the refrigerator for 10 to 15 minutes to firm the dough up.

Styling Tip

  • Want your cookies to look *EXACTLY* like mine, with a signature puddle of melted chocolate skimmed across each surface? Easy! Simply reserve a fève or a ½- to 1-inch piece of chopped chocolate for each cookie. Place on top of each cookie dough ball before baking. The chocolate will melt into the puddles you see on top of each cookie!

Baking Tip

  • I like to bake the cookies one pan at a time. I find that doing so makes the best cookies, ensuring that none of them have overly burnt bottoms or raw centers. However, to save time, you can bake two sheet pans at a time. Position a rack in the upper-third position of the oven, and a second one in the lower-third position of the oven. Bake a pan on each rack, swapping their positions half way through the Bake Time.
hand picking up rye chooclate chip cookie from a tray
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Get the Recipe: Super Chewy and Nutty Rye Chocolate Chip Cookies

Prep: 15 minutes
Cook: 10 minutes
Bake Time: 10 minutes
Total: 35 minutes
Servings: 16 cookies
Author: Michelle Lopez
This rye chocolate chip cookie recipe makes super nutty cookies with perfectly chewy centers and crispy edges! Rye flour in the recipe (and resting the dough overnight) makes the cookies extra chewy and flavorful.
(5 stars) 1 review
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Ingredients

  • 1 cup (4.5 ounces or 128 grams) all-purpose flour
  • ⅔ cup (2.45 ounces or 69 grams) rye flour
  • ½ teaspoon baking powder
  • ½ teaspoon baking soda
  • 1 teaspoon kosher salt
  • ¾ cup tightly packed (5.65 ounces or 160 grams) light or dark brown sugar
  • ¼ cup (1.75 ounces or 50 grams) granulated sugar
  • ½ cup (1 stick or 4 ounces or 113 grams) unsalted butter, melted and cooled slightly
  • 1 large egg, at room temperature
  • 2 teaspoons pure vanilla extract
  • 4 ounces (113 grams) dark chocolate (between 60% and 70% cocoa), from whole fèves or a high-quality chocolate bar, chopped into ½- to 1-inch pieces
  • 4 ounces (113 grams) milk chocolate (between 30% and 40% cocoa), from whole fèves or a high-quality chocolate bar, chopped into ½- to 1-inch pieces

Instructions
 

  • Mix the dry ingredients. In a small bowl, whisk together the flour, baking soda, baking powder, and kosher salt.
  • Mix the butter, sugars, egg, and extract. In a medium bowl, use a rubber spatula to mix together the butter and sugars until moistened, about 1 minute. Add the egg and vanilla extract and mix until combined.
  • Add the dry ingredients and chocolate. Gradually mix in the dry ingredients until just combined. Add both the dark and milk chocolate all at once and mix until the chocolate is evenly distributed throughout, about 1 minute.
  • Assemble the cookies. Use a 3-Tablespoon cookie dough scoop to portion the cookie dough into balls on a parchment-lined sheet pan.
  • Refrigerate the cookie dough balls overnight. Loosely cover the cookie dough balls with plastic wrap and refrigerate for at least 4 hours, preferably overnight.
  • When ready to bake the cookies, defrost the cookies, and prep the oven and baking pans. Remove the cookie dough from the refrigerator and set on the counter to thaw slightly while you preheat the oven.
    Position a rack in the center of the oven and preheat the oven to 350°F. Line two half sheet pans with parchment paper.
  • Bake the cookies. Bake one pan at a time for 10 minutes, or until the edges have set but the centers are still gooey.
    Cool the cookies on the pan on a wire rack for 20 minutes, or until the edges and bottoms of the cookies have set and feel firm to the touch.
    Repeat with the remaining cookie dough.
  • Serve and store. Serve warm or at room temperature. The cookies can be stored in an airtight container or zip-top bag at room temperature for up to 3 days.

Notes

  • To save myself some clean up, I melt the butter in the bowl I’m planning to make the cookie dough in. Specifically: I use a small bowl to mix the dry ingredients. Then, I use the microwave to melt the butter in a medium bowl big enough to mix the dough in, add the sugars, egg, and extract, then the dry ingredients and chocolate. As a result, I only need two bowls for this recipe!
  • When prepping ingredients, I also melt the butter first. That way, it has time to cool while I prep the rest of the ingredients. Doing so ensures your butter isn’t too hot and won’t scramble the egg when you add it to the dough!
  • Be mindful when melting the butter for these cookies! You don’t want the butter to sizzle, crackle, or pop. I like to chop it up into 1-inch cubes then melt it in a small sauce pot over medium-low heat. Be sure to stir the butter constantly as it melts to help prevent it from overheating.
  • If your dough seems too soft to scoop, don’t panic! It’s likely that the butter was still too hot when you combined it with the rest of the ingredients. Simply pop the bowl of cookie dough in the refrigerator for 10 to 15 minutes to firm the dough up.
  • Want your cookies to look *EXACTLY* like mine, with a signature puddle of melted chocolate skimmed across each surface? Easy! Simply reserve a fève or a ½- to 1-inch piece of chopped chocolate for each cookie. Place on top of each cookie dough ball before baking. The chocolate will melt into the puddles you see on top of each cookie!
  • I like to bake the cookies one pan at a time. I find that doing so makes the best cookies, ensuring that none of them have overly burnt bottoms or raw centers. However, to save time, you can bake two sheet pans at a time. Position a rack in the upper-third position of the oven, and a second one in the lower-third position of the oven. Bake a pan on each rack, swapping their positions half way through the Bake Time.
Did you make this recipe?Please leave a star rating and review in the form below. I appreciate your feedback, and it helps others, too!
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