The Best Gooey Sourdough Discard Chocolate Chip Cookies (Made with Almond Flour!)

If you have sourdough discard sitting in your refrigerator and you're wondering what to do with it, this recipe might become your new favorite.

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I recently experimented with a healthier version of chocolate chip cookies using sourdough discard and almond flour, and the results were honestly surprising. These cookies came out incredibly soft, rich, and gooey in the center—without using any traditional flour. In fact, they may be one of the best homemade cookies I've ever made.

Unlike many gluten-free cookies that can turn out dry or crumbly, these stay moist and chewy thanks to the combination of almond flour, sourdough discard, butter, and an extra egg yolk. The slight tang from the sourdough perfectly balances the sweetness of the chocolate chips, creating a cookie that tastes indulgent while using simple, wholesome ingredients.

Why You'll Love These Cookies

✔ Gluten-free (if your sourdough discard is gluten-free- mine is not, so there was some flour in the cookies)

✔ Made with nutrient-dense almond flour

✔ Uses up leftover sourdough discard

✔ Soft, gooey, and chewy texture

✔ Easy to make in one bowl

✔ No complicated ingredients

Whether you're enjoying them fresh out of the oven with a glass of milk or serving them as a healthier dessert option for your family, these cookies are guaranteed to disappear quickly.

Why Almond Flour?

Almond flour is one of my favorite alternatives to traditional flour because it's naturally rich in healthy fats, vitamin E, magnesium, and protein, and it's low carb. It also gives baked goods a softer texture and slightly nutty flavor that pairs perfectly with chocolate.

👉 Almond flour

The Secret to the Gooey Texture

There are three simple tricks that make these cookies extra gooey:

1. An Extra Egg Yolk

The additional yolk adds richness and helps create a soft, fudgy center.

2. Honey or Maple Syrup

A small amount of natural sweetener helps retain moisture and keeps the cookies soft even after they've cooled.

3. Slightly Underbaking

The cookies may look a little underdone when you remove them from the oven—and that's exactly what you want. They continue baking on the hot cookie sheet as they cool.

Gooey Sourdough Discard Almond Flour Chocolate Chip Cookies

Ingredients

• 1¾ cups almond flour

• ½ cup sourdough discard

• 6 tablespoons melted butter (or coconut oil)

• 1 whole egg

• 1 egg yolk

• ¼ cup Truvia Brown Sugar

• 1 tablespoon honey

• 1 teaspoon vanilla extract

• ¼ teaspoon baking soda

• ¼ teaspoon sea salt

• ¾–1 cup sugar free chocolate chips

  
  

Products I used:

👉 Almond flour 

👉 Sugar free chocolate chips

👉 Truvia Brown Sugar substitute

👉 Baking soda (aluminum free)

Instructions

Step 1

Preheat your oven to 350°F and line a baking sheet with a Silpat

Step 2

In a large bowl, whisk together:

• Melted butter

• Brown sugar

• Honey

• Whole egg

• Egg yolk

• Vanilla extract

• Sourdough discard

  
  

Mix until smooth.

Step 3

Add:

• Almond flour

• Baking soda

• Sea salt

  
  

Stir until fully combined.

Step 4

Fold in the chocolate chips.

Refrigerate the dough for 10-15 minutes. This gives the almond flour time to absorb moisture and creates a better cookie texture (don't skip this step!).

Step 5

Scoop the dough into approximately 12 cookies and place them on the baking sheet. Keep them slightly thick rather than flattening them too much.

Step 6

Bake for 10-11 minutes.

The edges should just begin turning golden while the centers still appear slightly underdone. Do not overcook!

Step 7

Remove from the oven and allow the cookies to cool on the baking sheet for 10–15 minutes before transferring them.

Pro Tip

For the ultimate gooey cookie experience, enjoy them while they're still slightly warm. If you're eating leftovers the next day, microwave one cookie for about 8–10 seconds and it'll taste freshly baked all over again.

Final Thoughts

These cookies are proof that healthier ingredients don't have to mean sacrificing flavor or texture. The combination of almond flour, sourdough discard, and chocolate creates a cookie that's rich, satisfying, and incredibly gooey in the center.

Don't be surprised if they become your new favorite way to use up sourdough discard!

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