Cinnamon Apple Thumbprint Cookies

These Gluten-Free Cinnamon Apple Thumbprint Cookies are a seasonal twist on a classic cookie! Traditional thumbprints are usually filled with a fruit jam, but instead these have a delicious cinnamon apple filling and drizzled with icing. Easier than pie, but just as sweet and satisfying. 

gluten-free cinnamon apple cookies thumbprint

Gluten-Free Cinnamon Apple Cookies!

It’s holiday baking season again and these cookies are a buttery, melt in your mouth, cozy treat that warms you up with the flavor of cinnamon apples. They’re filled with flavor from fresh apples and cinnamon as you bite into a pillowy soft gluten-free cookie dough.

A gluten & dairy free cookie perfect for baking around the holidays, during apple season or any time in between!

What Ingredients Do I Need to Make These Cinnamon Apple Thumbprint Cookies?

There are 3 steps to this recipe, but I promise each one is very quick & simple. You’ll need to make the cookie dough, cinnamon apples, and icing separately.

Here’s what you’ll need for the gluten-free thumbprint cookie dough:

  • Gluten-Free All Purpose Flour Mix. I used King Arthur Measure for Measure gluten-free flour and it created the fluffiest cookie dough base! I usually get a giant bag at Costco, but you can find this flour in most grocery stores.
  • Egg
  • Sugar
  • Pure Vanilla Extract
  • Baking Powder
  • Salt
  • Butter. I used Earth Balance vegan butter to keep this recipe dairy-free.

Cinnamon Apple Filling:

  • Apples
  • Cinnamon
  • Brown Sugar
  • Salt
  • Water
  • Gluten-Free All Purpose Flour. This is for thickening; you could also use cornstarch, tapioca flour, or arrowroot.

Icing Drizzle:

  • Powdered(Confectioners) Sugar
  • Milk. Use unsweetened plant-based milk for dairy-free.

How to Make this Cinnamon Apple Thumbprint Cookie Recipe

Start by making the cinnamon apple filling. Dice the apples as small as you can because they need to fit in the thumbprint indents!

While you’re at it, you can easily double the filling recipe and use it for other things…think over yogurt or oatmeal for breakfast! Anything that could use some apple pie flavor.

Next, in a large mixing bowl, beat the butter and sugar until fluffy. Add the egg, vanilla and salt. Gradually add flour and baking powder and beat on low until the dough forms.

Scoop the dough into 1 inch balls and place 2 inches apart on the baking sheet. Press your thumbprint into each of the balls to flatten and create a well.

Fill each indent with a teaspoon of apple pie filling. Bake the cookies as directed and let cool before icing.

To make the icing, add confectioners sugar and milk to a small bowl and stir until smooth. Add milk as needed to create a consistency thin enough to drizzle. Using a spoon or a piping bag, drizzle the icing over the cookies and allow the icing to set before storing.

Tips and Suggestions for these Thumbprint Cookies

  • I used granny smith apples, but honeycrisp apples also work great for baking.
  • The apple filling can be made ahead and stored in an airtight container in the fridge until ready to bake.
  • If you want a variety of cookies, go ahead and add your favorite jam to the thumbprint for some of the cookies. You’ll have 2 different versions baked at one time!

Looking for more gluten-free baking recipes? Check out some of these holiday favorites!

I hope you love these cookies as much as we do! If you’ve tried this recipe, be sure to tag me on instagram @thrivingglutenfree so I can see how it turned out!

Get your apples ready and let’s bake!

Cinnamon Apple Thumbprint Cookies

Course: Dessert
Cuisine: American
Keyword: apples, cinnamon apple, cookies


Cookie Batter

  • 1- 3/4 cups GF flour mix We used King Arthur Measure for Measure
  • 1/2 tsp baking powder
  • 1/2 tsp salt
  • 1-1/2 sticks vegan butter
  • 2/3 cup sugar
  • 1 egg
  • 1 tsp pure vanilla extract

Cinnamon Apple Filling

  • 2 apples peeled & very finely diced
  • 1/2 tsp cinnamon
  • 2 tbsp brown sugar
  • 2 tbsp water
  • 1/4 tsp salt
  • 2 tsp GF 1 to 1 flour you can also use cornstarch or tapioca flour

Icing Drizzle

  • 1/2 cup powdered sugar
  • 2 tsp plant based milk or until thin enough to drizzle


  • Preheat oven to 350° and line 2 baking sheets with parchment paper.

Make the Filling:

  • In a shallow stove top skillet, mix apples, cinnamon, sugar, water and salt over low-med heat. Simmer until apples are softened about 10 minutes.
  • Stir in flour and mix well until sauce is thickened. Remove from heat and set aside.

Make the Dough:

  • In a large mixing bowl, beat the butter and sugar until light and fluffy. Add egg, vanilla and salt.
  • Gradually add flour and baking powder and beat on low until combined and dough forms.
  • Scoop the dough into 1 inch balls and place 2 inches apart on baking sheet. Press thumbprint into each of the balls.
  • Fill each indentation with about a teaspoon of apple filling.
  • Bake cookies for 12-15 minutes until golden.
  • Cool completely about 30 minutes.

Make the Icing:

  • In small bowl, stir drizzle ingredients until smooth, if necessary, adding 1/2 teaspoon milk at a time until thin enough to drizzle.
  • Drizzle over cookies. Let stand about 15 minutes until set.


Store in an airtight container for up to 5 days or freeze up to 3 months.
Tried this recipe?Mention @thrivingglutenfree or #thrivingglutenfree!

Craving more gluten-free desserts? Check out these easy recipes!

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