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    Home ยป Gluten Free Baking Recipes

    Gluten Free Apple Pie Thumbprint Cookies

    Nov 6, 2025 by Thriving Gluten Free ยท This post may contain affiliate links ยท Leave a Comment

    Jump to Recipe Print Recipe

    These Gluten Free Apple Pie 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.ย 

    gluten-free apple pie thumbprint cookies

    Gluten Free Apple Pie 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 free and dairy free cookie recipes perfect for baking around the holidays, during apple season or any time in between!

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

    There are 3 steps to this recipe, but I promise each one is very quick and 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 Apple Pie 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 all at the same time!

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

    • Buttery Spritz Cookies
    • Gluten-Free Italian Pizzelles
    • Gingerbread Crinkle Cookies
    • Festive Holiday Peppermint Bark

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

    Get your apples ready and let's bake!

    gluten free apple pie thumbprint cookies
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    Apple Pie Thumbprint Cookies

    These Gluten Free Apple Pie 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.ย 
    Prep Time30 minutes mins
    Cook Time15 minutes mins
    Total Time45 minutes mins
    Course: Dessert
    Cuisine: American
    Keyword: apples, cinnamon apple, cookies

    Equipment

    • Baking Sheet
    • Stand Mixer

    Ingredients

    Cookie Batter

    • 1- ยพ cups Gluten Free 1:1 Flour
    • ยฝ teaspoon Baking Powder
    • ยฝ teaspoon Salt
    • 1-ยฝ sticks Butter use plant-based for Dairy Free
    • โ…” cup Sugar
    • 1 Egg
    • 1 teaspoon Vanilla Extract

    Cinnamon Apple Filling

    • 2 Apples peeled & very finely diced
    • ยฝ teaspoon Cinnamon
    • 2 tablespoon Brown sugar
    • 2 tablespoon Water
    • ยผ teaspoon Salt
    • 2 teaspoon GF Flour Blend you can also use cornstarch or tapioca flour

    Icing Drizzle

    • ยฝ cup Powdered Sugar
    • 2 teaspoon Milk or until thin enough to drizzle; use plant-based unsweetened for DF

    Instructions

    • Preheat oven to 350ยฐ 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 ยฝ teaspoon milk at a time until thin enough to drizzle.
    • Drizzle over cookies. Let stand about 15 minutes until set.

    Notes

    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 delicious gluten free desserts? I think you'll love these recipes too!

    • Peach Cobbler Skillet
    • Sweet Loren's S'mores Cookie Bake
    • The Best Gluten-Free Apple Crisp Recipe

    More Gluten Free Baking Recipes

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      Easy Gluten Free Chocolate Mug Cake (Ready in 1 Minute!)
    • gluten free gingersnaps cookie recipe
      Gluten Free Spiced Wafer Cookies (Copycat Sweetzels & Ivins Recipe)
    • gluten free gingerbread recipe
      Moist and Delicious Gluten Free Gingerbread Loaf
    • gluten free zucchini muffins with chocolate chips recipe
      Gluten Free Chocolate Chip Zucchini Muffins

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    thriving gluten free recipes for those with celiac disease and gluten intolerance

    Hi, I'm Debby! The recipe creator, mom and blogger behind Thriving Gluten Free. Our oldest daughter was diagnosed with Celiac Disease in 2011, so we've been navigating gluten-free living ever since. Here, we share our favorite recipes, products and tips to help make your gluten-free life easy, healthy and delicious!

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