Gluten-Free Pumpkin Chocolate Chip Cookies Recipe

This gluten-free pumpkin cookies recipe combines maple-scented pumpkin puree with quinoa flour, semi-sweet chocolate chips, and a silky brown sugar icing. Make them with canned or homemade pumpkin puree; they stay soft and tender whether you choose fresh or store-bought.

We made these cookies to use up leftover pumpkin and they were a hit at a family gathering. Kids enjoyed decorating each cookie with the brown sugar icing right before eating — an easy, fun activity that made the dessert table a favorite stop. The cookies are delightful without icing, but the brown sugar glaze brings a caramel-like richness that complements the nutty flavor of quinoa flour.

For consistent texture, canned pumpkin puree is a convenient choice because it is thicker and measured consistently. If you prefer, roast and puree fresh winter squash or pumpkin; some cooks favor squash for its slightly sweeter profile. Either way, aim for a thick, not watery, puree so the batter stays balanced.

These cookies are especially good during pumpkin season, but they work any time you want a cozy, autumn-flavored treat. They freeze well and make a satisfying afternoon snack or a dessert for gatherings. Below you’ll find the full recipe, ingredient list with optional glaze, and clear baking instructions so you can recreate them at home.

Recipe

Gluten-Free Pumpkin Cookies Recipe with Chocolate Chips and Brown Sugar Icing

5 from 1 review

Author: Rebecca Baron
Prep Time: 20 minutes
Cook Time: 10 minutes
Total Time: 30 minutes
Yield: 18 cookies
Category: Dessert
Cuisine: Gluten-Free

Description

This recipe creates soft, tender gluten-free pumpkin cookies using quinoa flour and oat flour for a nutty, wholesome bite. Semi-sweet chocolate chips add pockets of melty chocolate, while the optional brown sugar icing offers a caramelized sweetness that pairs perfectly with pumpkin spice. The cookies are soft and pillowy—ideal warm from the oven or at room temperature.

Ingredients

1 cup unsalted butter, softened
1 cup brown sugar, lightly packed
1 cup pumpkin puree (canned or homemade)
1 ½ teaspoons vanilla extract
1 large egg
1 ½ cups quinoa flour
½ cup gluten-free oat flour plus 2 tablespoons oat flour
1 teaspoon baking powder
1 teaspoon baking soda
¼ teaspoon salt (real salt)
1 tablespoon tapioca flour or arrowroot starch
1 ½ teaspoons ground cinnamon
1 cup semi-sweet chocolate chips

Optional Brown Sugar Icing

3 tablespoons butter
½ cup brown sugar
2 tablespoons milk (dairy or plant-based)
¾ cup powdered sugar

Instructions

Preheat the oven to 350°F (175°C). Line two baking sheets with parchment paper.
In a mixing bowl, beat the softened butter and brown sugar until the mixture is light and fluffy, about 2–3 minutes.
Beat in the pumpkin puree, vanilla, and the egg until well combined.
In a separate bowl, whisk together quinoa flour, oat flour, baking powder, baking soda, salt, tapioca flour (or arrowroot), and cinnamon.
Fold the dry ingredients into the butter-pumpkin mixture, mixing until just combined. Stir in the chocolate chips to distribute evenly.
Using a rounded scoop or spoon, drop rounded tablespoonfuls of batter onto the prepared baking sheets about 1½ inches apart. For small cookies use about 2 tablespoons batter; for larger cookies use about 4 tablespoons.
Bake for about 10 minutes, or until the tops are set but still very soft. Larger cookies may need a few additional minutes. Allow cookies to cool on the baking sheet for a few minutes, then transfer to a wire rack to cool completely.
If using, prepare the brown sugar icing and drizzle it over cooled cookies.
Store cookies in an airtight container at room temperature for several days, or refrigerate to extend freshness.

Brown Sugar Icing Instructions

Melt the butter in a small saucepan over medium-high heat. Allow it to foam and begin to brown slightly; it will develop a nutty aroma. Remove from heat immediately.
Stir in the brown sugar until combined and smooth.
Transfer to a bowl and whisk in the milk until the mixture is smooth.
Add the powdered sugar and whisk until the icing is thick and glossy. Let it sit 4–5 minutes to thicken slightly.
Drizzle the icing over cooled cookies and allow it to set before serving.

Tips & Notes

For consistent results, use canned pumpkin puree when you want a predictable texture. If you roast and puree fresh pumpkin or winter squash, make sure it is well-drained and not watery. Quinoa flour lends a slightly nutty flavor—if you prefer a milder taste, increase oat flour slightly and reduce quinoa flour. Cookies can be frozen in an airtight container for up to one month; thaw at room temperature or warm briefly in the oven.

To make the cookies dairy-free, substitute dairy-free butter and use a plant-based milk in the icing. Adjust baking time for larger cookies and always allow cookies to set briefly on the baking sheet before moving to a rack.