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These apple butter thumbprint cookies are easy to make and so delicious. They are filled with apple butter before baking and also rolled in cinnamon sugar, which adds a beautiful crunch. The apple butter and cinnamon sugar give them a wonderful apple pie spice flavor. You might even want to call them an apple butter snickerdoodle cookie! Thumbprint cookies are simple to make, as well as fun, and everyone is going to enjoy these delicious gluten free thumbprint cookies.

Apple butter thumbprint cookies with cinnamon sugar.

If you’re looking for a recipe for apple butter cookies, you’re going to love these. They boast the flavors of apples and cinnamon in every delicious bite.

If you’re craving chocolatey goodness, these Chocolate Chip Brownie Swirl Cookies and Chocolate Pistachio Eclairs will satisfy your sweet tooth. Or how about these Raspberry Jam Buttercream Cookies or Strawberry Mousse Tartlets for another fruity dessert?

A white plate with apple butter thumbprint cookies and cinnamon sticks on it.

Why You’ll Love Them

Gluten free and egg free:  Because there’s no gluten or egg in these cookies, they’re great for anyone following a special diet. There’s nothing missing from the flavor though, and these make a wholesome treat for everyone.
Simple to make: There’s nothing difficult about making gluten free thumbprint cookies, and the recipe is easy enough for baking newbies.
Really delicious: The apple butter and cinnamon sugar gives these little treats an amazing flavor. One of these apple butter snickerdoodle cookies is never enough!

A stack of gluten free thumbprint cookies next to a jar of apple butter.

Ingredients for Thumbprint Cookies with Apple Butter

You will need almond flour (or another GF flour), tapioca flour, salt, unsalted butter, maple syrup, vanilla extract, granulated sugar, cinnamon, and apple butter to make the cookie dough, filling and cinnamon sugar coating.

A bowl of gluten free granola ingredients.

For more detailed instructions with weights and measurements, jump to the printable recipe card.

Make the cookie dough:  Mix the almond flour with the tapioca flour and salt, and then add room temperature butter, maple syrup and vanilla extract, mixing until you have a dough consistency.
Make the cinnamon sugar: Mix the cinnamon with the granulated sugar.
Shape the cookies: Roll small portions of the cookie dough into balls then roll each one in the cinnamon sugar mixture, and put them on a parchment paper lined baking sheet.
Add the apple butter: Press down on each of the gluten free thumbprint cookies and add apple butter to the indentations.
Chill and bake: Chill the cookies in the freezer or refrigerator, then preheat the oven and bake until golden brown. Let the baked thumbprint cookies cool slightly and then transfer to a wire rack to cool completely.

A plate of gluten-free cookies with a spoon on top of them.

Substitutions and Variations

You can use your favorite kind of gluten free flour instead of the almond flour if you want, and either make your own apple butter or use store bought apple butter. Sub dark brown sugar for some of the granulated sugar if you like, or vegan butter for the unsalted butter.

Thumbprint cookies cooling on a rack.

You can get tapioca flour online (here), but if you prefer, you can use the same amount of cornstarch. Almond extract works in place of the vanilla extract. As for the apple butter, feel free to substitute apricot jam or even Nutella!

A plate of gluten free cookies with a bite taken out of it.

How to Serve GF Thumbprint Cookies

Let the gluten free thumbprint cookies cool completely before serving, so they don’t crumble and fall apart. They’re great served with anything from a glass of milk to a coffee.

And if you love these gluten free thumbprint cookies, you might also love raspberry hazelnut cookies or any of these thumbprint cookie recipes.

A plate of apple butter cookies with a bite taken out of it.

How to Store Gluten Free Thumbprints Cookies

Store:  Leftovers keep best on a platter with a clean kitchen towel on top at room temperature. They’ll start to soften within a day or so, especially if you choose to keep them in an airtight container instead, but will keep for 3 or 4 days.
Freeze: Freeze thumbprint cookies for up to 3 months. You can also prepare the dough and shape the cookies and freeze them unbaked for about the same amount of time, thawing them overnight in the refrigerator before continuing with the recipe.

A stack of apple butter cookies with a bite taken out of the top.

Apple Butter Filled Cookies FAQs

What can you use instead of your thumb to indent these?

If you don’t want to use your thumb or you have long nails, you can always use the back of a teaspoon size measuring spoon instead.

What should you do if the dough is too soft to roll into balls?

The best thing to do would be chilling it for 20 minutes in the refrigerator to firm it up.

Apple butter cookies on a plate with a spoon and a bowl of brown sugar.
5 from 44 votes

Apple Butter Thumbprint Cookies

By: Bella Bucchiotti
These delicious apple butter thumbprint cookies make a tasty treat. They have an apple butter-filled center and cinnamon sugar coating.
Prep Time: 15 minutes
Cook Time: 20 minutes
Cool Time: 30 minutes
Total Time: 1 hour 5 minutes
Servings: 26 Cookies


  • 2 ⅓ Cups almond flour
  • ½ Cup tapioca flour
  • ¼ Teaspoon salt
  • 4 Tablespoons butter, melted and slightly cooled
  • 6 Tablespoons maple syrup
  • 1 ½ Teaspoons vanilla extract
  • Cup granulated sugar
  • 1 ½ Teaspoons ground cinnamon
  • Cup apple butter


  • Preheat your oven to 325 degrees F and line a large baking sheet with parchment paper. Whisk together the almond flour, tapioca flour, and salt until well mixed.
  • Add the melted butter, maple syrup, and vanilla and mix until you have a cohesive cookie dough. No need to worry about overmixing! Set your dough aside for a moment.
  • In a wide shallow bowl, mix together the granulated sugar and ground cinnamon.
  • Using a small cookie scoop or a tablespoon measure, scoop up portions of the dough, gently roll into a ball in your hands, then roll to coat in the cinnamon sugar. Place the dough onto your prepared baking sheet. Continue with the remaining cookie dough, making sure to leave at least 1-inch between each cookie.
  • Using your thumb, gently press down into the center of each cookie to create an indentation. Make sure you don’t press all the way down to the baking sheet.
  • Fill each indentation with apple butter. Once all of your cookies are filled, place the entire baking sheet in the freezer for 10 minutes or the fridge for 30 minutes until the dough is firm to the touch.
  • Bake the cookies in your pre-heated 325 degree F oven for 18 to 20 minutes or until the bottoms are golden. Cool the cookies on the baking sheet for 10 minutes before moving them to a rack to cool completely.


  • If your kitchen is warm and the dough doesn’t seem thick enough to roll into balls, place it in the fridge for 15-20 minutes to firm up before scooping and rolling. 
  • If you cannot find tapioca flour, you can substitute an equal amount of cornstarch.  


Calories: 95kcal | Carbohydrates: 12g | Protein: 2g | Fat: 5g | Saturated Fat: 0.4g | Polyunsaturated Fat: 0.01g | Monounsaturated Fat: 0.02g | Cholesterol: 0.3mg | Sodium: 26mg | Potassium: 18mg | Fiber: 1g | Sugar: 7g | Vitamin A: 5IU | Vitamin C: 0.03mg | Calcium: 31mg | Iron: 0.4mg
Like this recipe? Rate and comment below!

These delicious gluten free thumbprint cookies are so easy to make and the combination of apple butter and cinnamon gives them a rich apple pie spice flavor. One or two of these with your drink of choice makes a delicious snack. There is plenty of choice for gluten free baking these days, and these tasty baked cookies have to be one of the tastiest recipes of all!

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Bella Bucchiotti

Bella Bucchiotti is a Canadian-based syndicated food, travel, and lifestyle writer, photographer, and creator at xoxoBella. She founded xoxoBella in 2015, where she shares her love for food, dogs, sustainability, fitness, crafts, outdoor adventures, travel, and philanthropy to encourage others to run the extra mile, try new recipes, visit unfamiliar places, and stand for a cause. Bella creates stress-free and family-friendly recipes for weeknight dinners and festive feasts.


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