Homemade Apple Cinnamon Thumbprint Cookie Recipe

The most delicious gluten-free Apple Cinnamon Thumbprint Cookies: soft, chewy cookies filled with spiced apple jelly and finished with a sweet maple drizzle—an ideal fall treat.

Autumn has officially arrived, and there’s nothing I love more than filling the kitchen with the scent of baked apples and warming spices. These Apple Cinnamon Thumbprint Cookies capture all the best flavors of the season: cinnamon, nutmeg, maple, and fresh apple. They are naturally gluten-free thanks to almond flour and are soft and chewy with a buttery finish. A little spiced apple jelly in the center and a light maple icing on top make them a standout fall dessert that’s perfect for baking after an afternoon of apple picking or serving at holiday gatherings.

What You’ll Need to Make These Cookies

• Almond flour – gives the cookies a tender, slightly nutty texture while keeping them gluten-free.
• Oat flour – helps prevent the cookies from becoming too dense or crumbly. If you don’t have oat flour, whole wheat flour, all-purpose flour, or a gluten-free flour blend will work. You can make oat flour at home by blending rolled oats until fine.
• Cinnamon and nutmeg – classic fall spices that enhance the apple and maple flavors.
• Butter or coconut oil – both produce a soft cookie, though butter delivers the richest flavor for a classic cookie texture.
• Maple syrup – a natural sweetener that contributes a warm maple note; honey can be substituted if needed.
• Apple butter (optional) – an extra boost of apple flavor and moisture; the cookies are excellent without it, but it’s a nice addition.
• Vanilla extract – a small amount enhances the overall flavor.
• Apple jelly – spiced apple jelly is ideal, but any jam or jelly you prefer will work for filling the centers.
• Walnuts (optional) – finely chopped walnuts add a pleasant crunch; pecans or almonds are good alternatives.

Recipe Overview

How to Make Apple Cinnamon Thumbprint Cookies

These cookies are straightforward to prepare and come together quickly with a short chill time. Follow these steps for consistent results:

1. Combine dry ingredients. In a large bowl, whisk together almond flour, oat flour, baking soda, cinnamon, and nutmeg. Set aside.
2. Cream the wet ingredients. In a separate bowl or in the bowl of a stand mixer, cream together the butter (or solid coconut oil), maple syrup, apple butter (if using), and vanilla until smooth. Gradually add the dry mixture and mix until a cohesive dough forms. Cover and chill the dough in the refrigerator for 30 minutes to make it easier to handle.
3. Prepare to shape. Preheat the oven to 350°F (175°C). Line two baking sheets with parchment paper or silicone baking mats. Use a small cookie scoop or a tablespoon to portion the dough into roughly 20 evenly sized balls.
4. Coat with egg white and nuts. Lightly beat one egg white in a small bowl. Place finely chopped walnuts in a separate bowl. Dip each dough ball into the egg white, then roll in the chopped walnuts, shaking off any excess. Arrange the coated balls on the prepared baking sheets, spaced about 2 inches apart.
5. Create the thumbprint and fill. Using a 1/2 teaspoon measuring spoon or your fingertip, press a shallow well into the center of each ball. Fill each well with spiced apple jelly or your choice of jam, about 1/2 teaspoon per cookie.
6. Bake and cool. Bake the cookies for 15–18 minutes, or until the edges are just beginning to turn golden. Let them rest on the baking sheet for 5 minutes to set, then transfer to a wire rack to cool completely. The centers will be soft when they first come out of the oven; this is normal and keeps them tender.
7. Drizzle with maple icing (optional). Once the cookies are cool, whisk together 1/2 cup powdered sugar, 2 tablespoons maple syrup, and 1/2 teaspoon water until smooth. Drizzle the icing over each cookie with a spoon or fork.

Tips for Best Results

• Chilling the dough helps the cookies hold their shape and makes rolling easier.
• If the dough feels too sticky, refrigerate until firm enough to scoop.
• Watch the bake time closely—overbaking dries the cookies. Remove when the edges are lightly golden.
• Store cooled cookies in an airtight container at room temperature for 3–4 days.

More Fall Recipes You’ll Love

• Pumpkin Bars with Cream Cheese Frosting
• Almond Flour Pumpkin Bread
• Pumpkin Spiced Cupcakes with Maple Cream Cheese Frosting
• Carrot Cake Oatmeal Breakfast Bars

I hope you enjoy these Apple Cinnamon Thumbprint Cookies. If you try the recipe, please leave a rating and share a photo using the hashtag #eatyourselfskinny—I love seeing your recreations!