Sourdough Rye Chocolate Chip Cookies

These Sourdough Rye Chocolate Chip Cookies are everything you want in a bakery-style cookie with crisp edges, chewy centers, pools of melted chocolate, and deep caramelized flavor from nutty brown butter.

Made with 100% rye flour, the rye gives them a softer texture and a more robust, almost malty flavor that makes them feel a little more grown-up without sacrificing any of the comforts of a classic cookie. You have to add these to your favorite list of sourdough cookies.

Follow my detailed instructions with photos and tips below to get the best sourdough rye chocolate chip cookies.

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👍 Why You’ll Love This Recipe

• A hearty, whole-grain twist on these popular Sourdough Discard Chocolate Chip Cookies that highlight rye flour.
• The cookies stay soft for days and the flavor develops even more as the dough rests.
• Balanced flavors with robust rye flour, tangy sourdough discard, bittersweet chocolate, and topped with flaky salt so they’re not too sweet.
• Big, gooey pools of chocolate chunks or chips in the cookies.
• No special equipment is needed.
• Brown butter adds a caramel, nutty flavor like in my Brown Butter Sourdough Oatmeal Raisin Cookies or Sourdough Cinnamon Rolls with Brown Butter Cream Cheese Frosting.

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🔍 Expert Baking Tips

• Use chopped chocolate for the best results. You’ll get puddles of large chocolate and smaller bits throughout in every bite.
• I use a mix of semisweet chocolate bars and chocolate wafers for different textures.
• Let the brown butter cool to room temperature before mixing in wet ingredients.
• Weigh your cookie dough balls so you get equal-sized cookies like I do for Sourdough Buckwheat Chocolate Chip Cookies.
• For perfectly circular cookies, swirl hot cookies in a cookie cutter to round the edges.
• Rest the cookie dough for at least 30 minutes for better flavor and easier shaping.

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🛠 Tools Needed

• Baking scale
  • Flour and sourdough starter can vary in weight from person to person, so weighing your ingredients is the best option! Measuring your ingredients by weight will make your baking more consistent and accurate.
• Sheet Pan, lined with parchment paper
• Spatula and Whisk, for mixing the cookie ingredients

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🛒 Ingredients Needed

See below for my ingredient recommendations and possible substitutions.

• Rye Flour
  • Like other ancient grains, rye flour has exceptional flavor that’s malty, aromatic, robust, and nutty.
  • I used King Arthur Medium Rye Flour in this recipe, but you can use dark rye flour too.
  • Other favorite ancient grain recipes include my Beginner’s Einkorn Sourdough Bread, Spelt Sourdough Bread, Einkorn Sourdough Sandwich Bread, and Emmer Sourdough Bread.
• Salt
• Baking Soda creates a chewy texture and helps the cookies spread.
• Unsalted Butter
  • Browning the butter adds caramel flavor to the cookies. It’s an easy trick for more flavorful baked goods, such as in these Sourdough Hot Cross Buns with Brown Butter or Sourdough Oatmeal Cream Pies.
• Vanilla Extract enhances flavor and adds warmth and perception of sweetness.
• Dark brown sugar
  • Brown sugar has molasses, which adds a little more richness to the cookies.
• Granulated sugar
  • Adds structure and sweetness to the cookies.
• Egg
  • Adds structure to help bind the ingredients together.
  • To make egg-free, substitute with an egg replacer or flax egg.
• Sourdough Discard
  • If you don’t have an active sourdough starter, learn how to make one in a week following my how-to guide. See my top sourdough starter tips and other sourdough discard recipes.
  • To make 100% rye, use a rye sourdough starter.
• Semisweet Chocolate
  • Chop real chocolate bars for the best flavor and texture in chocolate chip cookies! Brands I like include Baker’s, Guittard, Valrhona, or more commonly found Lindt or Ghirardelli.
  • You can also use bittersweet chocolate, dark chocolate, milk chocolate, or chocolate chips in you prefer.
  • Other favorite chocolate recipes include my Chocolate Sourdough Bread with Coffee, Sourdough Chocolate Muffins, and Sourdough Chocolate Brioche.

Variations

• Add ½ cup of toasted walnuts or pecans for crunch.
• Add 1 teaspoon of cinnamon, cardamom, or a mix of spices.
• For more brightness, zest an orange into the dough.
• Swap some of the chocolate chips for dried cherries for a sweet-tart contrast.

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🍪 How to Make Sourdough Rye Chocolate Chip Cookies

Follow this detailed recipe guide with step-by-step images as you make the best sourdough rye chocolate chip cookies.

1. Brown Butter

Melt the butter in a light-colored saucepan over medium heat so you can easily monitor the color. As it heats, the butter will foam and sizzle while the water cooks off, and the milk solids will begin to toast at the bottom of the pan.

Stir or swirl occasionally to keep everything cooking evenly. After a few minutes, the butter will turn a deep golden color and develop a rich, nutty aroma. Remove from the heat and pour it into a heatproof bowl right away to stop the cooking and prevent it from burning.

Let it cool to room temperature before using.

2. Mix the Dry Ingredients

As the butter cools, whisk the rye flour, salt, and baking soda together in a small bowl and set aside.

3. Mix the Wet Ingredients

In a large mixing bowl, whisk the cooled brown butter, sugars, egg, vanilla, and sourdough discard.

4. Mix the Cookie Dough and Rest

Add the dry ingredients to the bowl and mix until mostly incorporated.

Then, fold in the chopped chocolate chunks with a spatula.

Cover and refrigerate the cookie dough for at least 30 minutes to infuse the flavors and make shaping easier.

5. Bake

Preheat the oven to 350ºF (177ºC) and line baking sheets with parchment paper to prevent sticking.

Scoop out 2 TBS of cookie dough, or about 45g each. Roll into balls and place a few inches apart on the prepared pans.

For large pools of chocolate, chop large chunks of chocolate and stick on top. Sprinkle with optional flaky salt.

Bake for 12-13 minutes or until the cookies are just set around the edges. Give the pan a light tap on the counter a couple of minutes before they’re done baking and after they’re baking to help flatten them.

Cool for at least 15 minutes on a wire rack.

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How to Store and Serve

• Store in an airtight container at room temperature for up to 3–4 days
• For longer storage, freeze baked cookies for up to 2 months.
• Freeze cookie dough balls and bake fresh as needed. They may need a couple of more minutes in the oven.
• Let cookies cool completely before storing to keep edges crisp.
• Warm slightly before serving for gooey chocolate and best texture
• Pair with coffee, tea, or a glass of milk for a cozy treat.

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❓ Frequently Asked Questions