Healthy Apple Pie Thumbprint Cookies
Yields: 24 cookies
These cookies are perfect for when you’re craving apple pie but don’t want to make one entirely from scratch… Or want a little built-in portion control! They have the same sweet, buttery, and cozy flavors, but they require a fraction of the work to make! Leftover cookies will keep for at least one week if stored in an airtight container in the refrigerator.
  • for the cookies
  • 1 cup (120g) white whole wheat flour or gluten-free* flour (measured like this)
  • 1 tsp cornstarch
  • ¾ tsp baking powder
  • ⅛ tsp salt
  • 1 ½ tbsp (21g) unsalted butter or coconut oil, melted and cooled slightly
  • 1 large egg white, room temperature
  • 1 ½ tsp vanilla extract
  • ½ cup (96g) coconut sugar
  • for the filling
  • ½ cup (60g) very finely diced apple
  • ¼ tsp ground cinnamon
  • 1 tsp pure maple syrup
  1. To prepare the cookie dough, whisk together the flour, cornstarch, baking powder, and salt in a medium bowl. In a separate bowl, whisk together the butter, egg white, and vanilla. Stir in the coconut sugar. Add in the flour mixture, stirring until incorporated. Chill the cookie dough for 30 minutes.
  2. While the cookie dough chills, prepare the filling. Add the apples and cinnamon to a small pan lightly coated with cooking spray, and cook over medium-low heat for 3-5 minutes, or until the apples are tender. Transfer to a small bowl to cool. Once at room temperature, stir in the maple syrup.
  3. Preheat the oven to 350°F, and line a baking sheet with a silicone baking mat or parchment paper.
  4. Drop the cookie dough into 24 small rounded mounds on the prepared baking sheet. Using your index finger or thumb, make an indentation in the center of each. (If the dough cracks, gently pinch it back together with your fingers. If the cookie dough sticks to your fingers, moisten them with a small amount of water!) Carefully spoon in a small amount of filling, and gently press it down into the cavity with a spatula.
  5. Bake at 350°F for 8-10 minutes. Cool on the baking sheet for 10 minutes before carefully transferring to a wire rack. (If the cookies stick to the baking sheet, slide a knife underneath each first!)
Notes: For the gluten-free flour, use as follows: ¼ cup (30g) millet flour, ¼ cup (30g) tapioca flour, 3 tablespoons (21g) coconut flour, and ¾ teaspoon xanthan gum. Most store-bought gluten-free flour blends will work as well, if measured like this.

Whole wheat pastry flour, regular whole wheat flour, or all-purpose flour may be substituted for the white whole wheat flour.

The cornstarch helps keep the cookies soft.

Brown sugar or granulated sugar may be substituted for the coconut sugar.

Honey or agave may be substituted for the pure maple syrup.

I used a Fuji apple, and I did not peel it. Most firm red apples will work! The apples should be cut even smaller than the size of miniature chocolate chips. Yes, I know it takes extra time and effort, but I promise it’s worth it! This small size ensures the apples will soften more while baking.

The filling does not spread while baking, so you must gently pat it down with a spatula. If you prefer more filling, then double the amounts!

This recipe is easily doubled!

{gluten-free, clean eating, low fat}
Recipe by Amy's Healthy Baking at