These Gluten-Free Sourdough Discard Mini Pecan Pie Cookies are soft, buttery, slightly chewy, and filled with a rich, gooey pecan topping. They’re a delicious way to use up gluten-free sourdough discard while enjoying all the cozy flavors of pecan pie in a small, easy-to-make cookie.

Ingredients

For the Gluten-Free Cookie Dough

• ½ cup (113 g) unsalted butter, softened
• ½ cup (100 g) packed brown sugar
• ¼ cup (50 g) granulated sugar
• 1 large egg yolk
• 1 teaspoon vanilla extract
• ½ cup (120 g) gluten-free sourdough discard
• 1 ¾ cups (210 g) gluten-free 1-to-1 all-purpose flour blend
• ½ teaspoon baking soda
• ¼ teaspoon salt
• ½ teaspoon ground cinnamon
• 1 tablespoon cornstarch
• 1–2 tablespoons milk, only if needed

For the Mini Pecan Pie Filling

• 1 cup (110 g) finely chopped pecans
• ⅓ cup (70 g) brown sugar
• ¼ cup (60 ml) maple syrup
• 2 tablespoons unsalted butter, melted
• 1 large egg yolk
• 1 teaspoon vanilla extract
• ¼ teaspoon cinnamon
• Pinch of salt

Important: If these cookies need to be strictly gluten-free, use a certified gluten-free flour blend, gluten-free sourdough starter/discard, and certified gluten-free ingredients as needed. Avoid cross-contamination from regular flour.

Instructions

1. Prepare the Gluten-Free Cookie Dough

Add the softened butter, brown sugar, and granulated sugar to a large mixing bowl.

Beat for about 2–3 minutes, until the mixture is creamy and slightly fluffy.

Add the egg yolk and vanilla extract. Mix until smooth.

Stir in the gluten-free sourdough discard until well combined.

In a separate bowl, whisk together the gluten-free flour blend, baking soda, salt, cinnamon, and cornstarch.

Gradually add the dry ingredients to the wet mixture. Mix just until a soft cookie dough forms.

Gluten-free dough can sometimes absorb moisture differently depending on the flour blend. If the dough seems unusually dry or crumbly, add 1 tablespoon of milk and mix. Add another tablespoon only if necessary.

2. Chill the Dough

Cover the bowl and refrigerate the dough for 30–45 minutes.

This step is particularly helpful for gluten-free cookies because it allows the flour to absorb the moisture from the sourdough discard and helps the cookies hold their shape.

3. Make the Pecan Pie Filling

While the dough chills, prepare the filling.

Add the chopped pecans, brown sugar, maple syrup, melted butter, egg yolk, vanilla extract, cinnamon, and salt to a small bowl.

Stir until the pecans are completely coated and the mixture becomes thick and sticky.

Set aside.

4. Shape the Mini Cookies

Preheat your oven to 350°F (175°C).

Line a baking sheet with parchment paper.

Scoop approximately 1½ tablespoons of chilled dough for each cookie.

Roll each portion gently between your palms to form a ball.

Place the balls on the prepared baking sheet, leaving about 2 inches of space between them.

Using your thumb or the rounded back of a small measuring spoon, gently press a deep indentation into the center of each cookie.

Be careful not to press all the way through the dough.

5. Add the Pecan Filling

Place about 1 teaspoon of pecan filling into the center of each cookie.

Try to keep the filling inside the indentation rather than spreading it over the cookie.

If the filling is particularly loose, use slightly less in each cookie.

6. Bake

Bake the cookies for approximately 11–14 minutes.

The edges should be lightly golden and the cookie centers should look set.

The pecan filling will be hot and bubbly when the cookies come out of the oven, so don’t worry if it looks slightly soft.

Remove the baking sheet from the oven and let the cookies cool for 5–10 minutes.

Then carefully transfer them to a wire rack.

The pecan filling will firm up as it cools.

Tips for the Best Gluten-Free Sourdough Cookies

Use a good gluten-free flour blend

A gluten-free 1-to-1 baking flour containing ingredients such as rice flour and starches works well.

If your flour blend already contains xanthan gum, you generally don’t need to add additional xanthan gum.

Don’t overmix

Once the flour has been incorporated, mix only until everything comes together. Overmixing isn’t necessary and can affect the final texture.

Chill the dough

Don’t skip the chilling step. Gluten-free dough can be softer and more delicate than conventional cookie dough, and chilling makes it much easier to handle.

Chop the pecans finely

Because these are mini pecan pie cookies, finely chopped pecans work better than large pieces. They fit neatly into the cookie centers and create a more balanced bite.

Watch the cookies near the end

Gluten-free cookies can go from lightly golden to overbaked fairly quickly. Remove them when the edges are set and lightly browned while the centers still look slightly soft.

Can I Use Gluten-Free Sourdough Discard Straight From the Refrigerator?

Yes. Cold gluten-free sourdough discard works well in this recipe.

Give the discard a good stir before measuring it because liquid can sometimes separate from the starter while it sits in the refrigerator.

Can I Use Active Gluten-Free Sourdough Starter?

Yes. You can use active gluten-free sourdough starter instead of discard in the same quantity.

The cookies don’t rely on the starter for leavening, so you don’t need to change the recipe.

Can I Make These Without Maple Syrup?

Yes. You can replace the maple syrup with light corn syrup or another thick liquid sweetener.

For a deeper caramel flavor, maple syrup is especially delicious with the brown sugar and pecans.

How to Store Gluten-Free Pecan Pie Cookies

Once completely cooled, place the cookies in an airtight container.

They can be stored at room temperature for approximately 2–3 days.

For longer storage, refrigerate them for up to 5 days.

Allow refrigerated cookies to sit at room temperature for a few minutes before serving, or warm them briefly in the microwave.

Can You Freeze Them?

Yes.

Place completely cooled cookies in a freezer-safe container with parchment paper between the layers.

Freeze for up to 2 months.

Thaw at room temperature before serving.

For a warm pecan-pie flavor, microwave a thawed cookie for approximately 8–10 seconds.

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Gluten-Free Sourdough Discard Mini Pecan Pie Cookies

Prep Time: 20 minutes
Chill Time: 30–45 minutes
Bake Time: 11–14 minutes
Total Time: About 1 hour 15 minutes
Servings: 18–22 mini cookies

Ingredients

Cookie Dough

• ½ cup unsalted butter, softened
• ½ cup brown sugar
• ¼ cup granulated sugar
• 1 egg yolk
• 1 teaspoon vanilla
• ½ cup gluten-free sourdough discard
• 1¾ cups gluten-free 1-to-1 flour
• ½ teaspoon baking soda
• ¼ teaspoon salt
• ½ teaspoon cinnamon
• 1 tablespoon cornstarch

Pecan Filling

• 1 cup finely chopped pecans
• ⅓ cup brown sugar
• ¼ cup maple syrup
• 2 tablespoons melted butter
• 1 egg yolk
• 1 teaspoon vanilla
• ¼ teaspoon cinnamon
• Pinch of salt

Directions

1. Cream butter, brown sugar, and granulated sugar until smooth.
2. Mix in egg yolk, vanilla, and gluten-free sourdough discard.
3. Whisk together flour, baking soda, salt, cinnamon, and cornstarch.
4. Gradually mix the dry ingredients into the wet ingredients.
5. Chill the dough for 30–45 minutes.
6. Mix all pecan filling ingredients in a small bowl.
7. Heat oven to 350°F (175°C) and line a baking sheet with parchment.
8. Roll dough into small balls and place on the baking sheet.
9. Press an indentation into each cookie.
10. Fill each center with about 1 teaspoon of pecan mixture.
11. Bake for 11–14 minutes, until lightly golden around the edges.
12. Cool for 5–10 minutes before transferring to a rack.
13. Allow the cookies to cool completely before storing.

Estimated Nutrition

Per cookie, assuming 20 cookies:

• Calories: 175–185
• Carbohydrates: 21 g
• Protein: 2 g
• Fat: 10 g
• Saturated Fat: 4 g
• Sugar: 11 g
• Fiber: 1–2 g
• Sodium: 75 mg

Nutrition values are estimates and can vary depending on the gluten-free flour blend and other ingredients used.