Brown butter rye chocolate chip cookies with crisp edges and puddings of chocolates. Rye flour and a hint of warm spices gives these cookies a delicious depth of flavor that regular chocolate chip cookies could never!

Calling all cookie monsters! These look like the classic chocolate chip cookies you grew up with, but one bite tells you something is different.
The combination of rye flour, semi-sweet and dark chocolate, plus a mixture of spices, makes these cookies special and unique. There is a toasty, almost malty flavor that makes people stop mid chew to ask what they’re tasting. Bu
If you don’t have rye flour, try these whole wheat chocolate chip cookies instead!

To me, the best kind of cookies are slightly crisp along the edges with a soft and chewy interior. There should be well distributed puddles of chocolate throughout. It should have a pleasant balance of sweet cookie dough with slightly bitter chocolate.
Ingredient Notes
Rye flour. Rye is a cousin of wheat and barley, best known for rye bread and rye whiskey. It comes in several grinds: white, medium, dark, and pumpernickel. I tested this recipe with King Arthur medium rye flour, which is milled with more of the bran than white rye. I highly recommend sticking with medium rye here; darker rye will make a denser, more assertive cookie.

Spices and coffee. You won’t taste cinnamon, nutmeg, or coffee individually. Together they amplify the nuttiness of the rye and brown butter and leave a lingering warmth. Ground nutmeg works if you don’t have whole.
Vanilla. Pure vanilla extract or vanilla bean paste both work.
Flaky salt. Use Maldon sea salt flakes for finishing. Don’t swap in kosher or table salt; they’re far saltier. No flakes? Just skip it this time.

Chocolate. Use what you love. I like a mix of 72% dark chocolate chunks and semi-sweet chips.
- Chips hold their shape (thanks to stabilizers and less cocoa butter) and distribute evenly.
- Chopped chocolate melts into irregular puddles and pockets. Splurge on a single-origin bar or chop up your favorite candy bar.

Not your traditional way to mix cookie dough
Most chocolate chip cookie recipes start by creaming together softened butter and sugar. This recipe is a little different.
First off, cold butter is added to the mixing bowl. No need to bring butter to room temperature to softened. Second, super hot liquid brown butter is poured over the cold butter-sugar mixture.Unlike other cookies, right?

- Place cold butter in mixing bowl along with sugar, brown sugar, vanilla paste, and spices. Pour hot liquid brown butter over butter-sugar mixture.
- Let mixture sit undisturbed for 5 minutes. The brown butter will bubble and foam. It’s normal.
- Use paddle attachment to beat mixture together for 2 minutes. The mixture will be dark in color and appear broken or oily on the surface.
- Add egg and egg yolk. Beat for 3 minutes until mixture is creamy in color and thickened in consistency.


- Add in the dry flour mixture all at once. Mix gently until there are no longer and dry streaks of flour.
- Fold in chocolate. Chill dough overnight.
Tips for Success
Don’t skip the chill. The dough will be very stick at first. The flour needs time to hydrate, and cold butter keeps the cookies from spreading into puddles. Rye flour especially benefits from the rest.
Soften before scooping. Fridge-cold dough is rock hard. Give it an hour on the counter rather than wrestling it.


Use a scoop for even baking. I use a size 24 scoop. Scoop sizes are numbered by how many scoops fill a quart, so a smaller number means a bigger scoop. Look for the number stamped inside the bowl of the scoop.
Let them set on the pan. Leave baked cookies on the hot sheet for 5 to 7 minutes before moving them. They firm up as they cool.


Storage and Make-Ahead
- Baked cookies: Best warm from the oven and within 2 days. Store in an airtight container for up to 5 days. Around day 4 they lose some chew but are still delicious.
- Fridge dough: Keep scooped dough balls tightly covered for up to 3 days.
- Freezer dough: Freeze scooped balls on a lined sheet for 1 to 2 hours until solid, then move them to a labeled zip-top bag for up to 4 months. Bake straight from frozen at 350°F for about 18 minutes, rotating halfway. No thawing needed. Easy peasy!


Rye Chocolate Chip Cookies

Ingredients
- 230 grams (2 ¼ cup) medium rye flour, *
- 1 tsp kosher salt
- ½ tsp baking soda
- 170 grams (12 Tbsp) unsalted butter, divided
- 150 grams (¾ cup) light brown sugar, packed
- 100 grams (½ cup) granulated sugar
- 2 tsp pure vanilla extract, or vanilla bean paste
- ½ tsp instant coffee granules
- ½ tsp ground cinnamon
- ⅛ tsp freshly grated nutmeg, or ground nutmeg
- 1 large egg
- 1 large egg yolk
- 150 grams chopped dark chocolate, or chocolate chips*
- Maldon sea salt flakes, for sprinkling
Instructions
- In a large bowl, whisk together rye flour, salt, and baking soda. Set aside.
- In the bowl of a stand mixer, add 56 grams (4 Tbsp) cold butter, brown sugar, sugar, vanilla, instant coffee granules, cinnamon, and nutmeg. Set aside.
- Melt remaining 114 grams (8 Tbsp) butter in a heavy bottomed sauce pot over medium heat. Occasionally swirl pot to ensure even heating. The mixture will bubble and foam as it cooks. The bubbling will be vigorous at first, but will subside and lessen as butter cooks.
- Continue to cook until butter smells nutty and the milk solids at the bottom of the pot have turned rich golden brown in color. Remove from heat and pour brown butter (along with browned milk solids) into stand mixer bowl over sugar mixture. Let sit for 5 minutes.
- Attach paddle to stand mixer. Beat mixture on medium speed for 2 minutes. Mixture will be dark in color and look broken or oily on the surface.
- Add egg and egg yolk. Beat on medium speed for 3 minutes until mixture is creamy in color and has thickened in consistency. Scrape down sides of bowl to ensure even mixing.
- Add dry flour mixture. Mix until just combined, and there are no longer any dry streaks of flour. Fold in chocolate until evenly distributed.
- Transfer dough to a clean bowl. Cover tightly with plastic wrap or lid. Chill in the fridge overnight, at least 6 hours.
- Remove dough from fridge and let sit at room temperature for 1 hour to soften. Use a size 24 scoop to portion out the cookie dough. Place scoops on a parchment lined baking sheet. Cover and place in the fridge while oven preheats.
- Preheat oven to 350°F. Line several baking sheets with parchment paper or reusable silicone baking mat.
- Place chilled cookie portions at least 3-inches apart on prepared baking sheet. Bake for 8 minutes. Rotate baking sheets. Bake for another 6-8 minutes until cookies have spread and are set along the edges.
- Immediately sprinkle hot cookies with sea salt flakes, if using. Allow cookies to remain on hot baking sheet for 5-7 minutes before using an offset spatula to transfer warm cookies to wire rack. Cool to room temperature or eat warm!
Notes
- Baking time refers to size 24 cookie scoop portions. Adjust cooking time should you choose to portion dough into a different size.
- Store cooled cookies in an airtight container for up to 5 days.
- This recipe was tested using King Arthur Baking Company Medium Rye Flour.
- Cinnamon and nutmeg add a subtle spice that works wonderfully with the nutty rye flour and brown butter
- Use any chocolate of choice. I used a combination of 72% dark chocolate chunks and semi-sweet chocolate chips.
- After scooping dough in Step 9, place covered cookie dough in the freezer for 1 to 2 hours until frozen. Remove from freezer. Transfer frozen cookie dough balls to a freezer zip-top bag. Frozen dough will keep in the freezer for up to 4 months.
- Place frozen scooped cookie dough on parchment lined baking sheet, spacing them about 3-inches apart. Bake in a preheated 350 degree F oven for 18 minutes, rotating pan midway through baking.
- Do not defrost or soften frozen cookie dough before baking. Bake directly from the freezer.
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.
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My children love chocolate chip cookies, definitely saving this one!
Great! I hope you give the recipe a try!