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Chocolate Chia Cookies (Gluten Free)

A healthy treat made with simple ingredients, these Chocolate Chia Cookies make the perfect morning snack!

gluten free chocolate chia cookies

Adding chia seeds certainly isn’t a requirement for making a delicious cookie. But I’ve added them in this recipe because of their added health benefits. According to the Academy of Nutrition and Dietetics:

Chia seeds have gained attention as an excellent source of omega-3 fatty acid. They also are an excellent source of dietary fiber at 10 grams per ounce (about 2 tablespoons), and contain protein and minerals including iron, calcium, magnesium and zinc.

I have found it harder to add fiber to baked goods when developing gluten free recipes. Most gluten free flour blends are low in fiber, so adding chia seeds to these cookies gives a much needed fiber boost.

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stack of gluten free chocolate chia cookies

Gluten Free Chocolate Chia Cookies

  • Author: Regan Jones, RD
  • Total Time: 20 min
  • Yield: 2 dozen cookies
  • Diet: Gluten Free


A healthy treat made with simple ingredients, these Chocolate Chia Cookies make the perfect morning snack!


  • 2 tablespoons warm water
  • 1 tablespoon ground flax seed
  • 1 1/2 cups sugar
  • 3/4 cup olive oil or melted coconut oil
  • 1 large egg, at room temperature
  • 2 tablespoons applesauce
  • 2 cups (240 g) all-purpose gluten-free flour
  • 1 teaspoon baking soda
  • 3/4 teaspoon kosher salt or sea salt
  • 2 tablespoon of chia seeds
  • 3 tablespoons unsweetened cocoa powder
  • 1 cup milk, semisweeet or dark chocolate chips


  1. Preheat oven to 375ºF. Combine water and flax in a small bowl; let stand until thickened, about 5 minutes.
  2. Add sugar, oil, egg, and applesauce to a large bowl; mix until combined. Add flax mixture, and stir until combined.
  3. Whisk together flour, baking soda, salt, chia seeds, and cocoa in a medium bowl. Add dry ingredients to sugar mixture; mix well. Stir in chocolate chips.
  4. Spoon cookie dough out onto a Silpat or parchment paper lined cookie sheet by rounded tablespoonfuls. Bake until lightly browned (centers will be soft), 10 to 13 minutes.
  5. Cool slightly on pan; transfer cookies to wire cooling rack to cool completely. Store in airtight containers.
  • Prep Time: 10 min
  • Cook Time: 10 min
  • Category: Dessert
  • Method: Baking
  • Cuisine: American


  • Serving Size: 1 cookie
  • Calories: 165
  • Sugar: 13 g
  • Sodium: 125 mg
  • Fat: 8 g
  • Carbohydrates: 21 g
  • Fiber: 1 g
  • Protein: 2 g

Keywords: Gluten Free Chocolate Chia Cookies

If you enjoyed these Chocolate Chia Cookies, try these:

gluten free small batch oatmeal chocolate chip cookies

Small Batch Gluten Free Oatmeal Chocolate Chip Cookies

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