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With a sweet little center filled with either jam or chocolate hazelnut spread, These Gluten Free Thumbprint cookies are a must make. These cookies have a crispy exterior with a chewy middle, are easy-to-prepare and perfect to make year round. The dough is made in 1-bowl and they are free from gluten, grains and refined sugar but still perfectly delicious.

Gluten free thumbprint cookies on a plate.Gluten Free Thumbprint Cookies

These Gluten Free Thumbprint cookies are the cutest little cookie! A perfectly textured thumbprint cookie filled with your choice of a sweet jam or Nutella middle. What we really love about this recipe is that it is truly easy to make. We simplified the steps needed to make this cookie by using just 1-bowl and a sturdy spoon to mix the dough all together. Which means you can have fresh, hot cookies on your table quickly. They don’t need to be chilled (but can be if you want to make the dough ahead of time) and don’t dirty up a lot of dishes. This is also a great recipe to make with the kids!

Here’s what you need to make them:

  • Almond Flour
  • Coconut Flour
  • Butter
  • Coconut Sugar
  • Vanilla Extract
  • Baking Powder
  • Salt
  • Jam (homemade or store-bought)
  • Nutella (homemade or store-bought)
Making a thumbprint in cookie dough.

Filling the Thumbprint Cookies

We’ve filled these cookies with a chocolate hazelnut spread (that can either be homemade or store-bought) and strawberry jam (again, homemade or store-bought). But let your imagination run wild and use whatever you’d like to make these thumbprint cookies. It could be fun to switch it up and fill it with a sweetened almond butter, pumpkin butter or even fill it with marshmallow cream before it is set up to make marshmallow thumbprint cookies! We can’t wait to see you’re creations.

Tips for Making Gluten Free Thumbprint Cookies

  1. Make sure your butter is fully softened. This recipe requires the butter to be room temperature because it is mixed in with the dough as is, as opposed to creaming it or melting it. Room temperature butter can easily be mixed into this almond flour dough, with no chunks of butter remaining.
  2. Use a study spoon and a bit of muscle.We use a bit of an unusual method of making this dough: all the ingredients are simply mixed together in a bowl until the dough has come together. It’s easiest to achieve smooth dough if you use a sturdy spoon, such as metal or wooden, and really mix up the dough well. At some point while you are making the dough you are going to feel like it won’t ever come together–but keep mixing: it will.
  3. Double indents! You’ll need to make an indent before the cookie is baked, and after. The cookies puff and spread slightly when baking, so when they come out of the oven, carefully use a teaspoon sized measuring spoon and press gently in the well to reform it.
Gluten free thumbprint cookies filled with Nutella and jam.

Storing Gluten Free Dough and Baked Cookies

The cookie dough can be made up to 3 days ahead of time. The dough can be frozen if desired, but portion them out and make the indentation before freezing.

As with any of our gluten-free cookie recipes, these are best eaten on the first or second day they are made. On day 1, the outside is crisp in the middle is soft and chewy. The cookies can be stored in a bag or container at room temperature for up to 2 days, but they soften as time goes on.

Gluten free thumbprint cookie recipe.

If you like this gluten free cookie recipe, check out these others:

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With a sweet little center filled with either jam or Nutella, These Gluten Free Thumbprint cookies are a must make. These gluten free cookies have a crispy exterior but a chewy middle, are easy-to-prepare and perfect year round. The dough is made in 1-bowl and they are free from gluten, grains and refined sugar but still perfectly delicious.
Prep Time 15 minutes
Cook Time 12 minutes
Total Time 27 minutes


  • 2 cups 198 grams almond flour
  • 2 tablespoons 14 grams coconut flour
  • 1/2 teaspoon baking powder
  • Pinch salt
  • ½ cup grass-fed butter room temperature
  • 1/2 cup coconut sugar
  • 1 teaspoon vanilla extract
  • Jam homemade or store-bought
  • Nutella homemade or store-bought


  • Preheat the oven to 350º and line a baking sheet with parchment parchment paper.
  • Whisk together almond flour, coconut flour, baking powder and pinch of salt in a bowl.
  • Add in butter, coconut sugar and vanilla extract. Mix the dough all together, using a sturdy spoon, until fully combined with no visible butter remaining.
  • Roll dough into balls about 1 tablespoons in size and place on baking sheet about 1-½” apart. Make an indentation with your thumb in the middle. If any cracks appear you can smooth them over with your finger.
  • Bake for 12 minutes. Remove from oven and using a teaspoon measuring spoon press down into the indentations to re-form the well. Let cool.
  • Meanwhile, heat nutella and or jam briefly in a small pot or in the microwave. Spoon the jam and or nutella into the wells of the cookies. Let set up before serving.


  1. This dough could also be made in an electric stand mixer, following the same process as mixing it by hand.
  2. If you find the dough difficult to work with, place in the refrigerator for 15-20 minutes before rolling cookie dough balls.
  3. Cookie dough can be made up to 3 days ahead. Fully baked cookies can be made up to 2 days ahead and stored at room temperature.
  4. This recipe was originally published in 2014 and republished with an updated recipes and photos in 2020.


Serving: 1cookieCalories: 109kcalCarbohydrates: 10gProtein: 1.2gFat: 7gSaturated Fat: 4gSodium: 79mgFiber: 1gSugar: 9g
Course: Dessert
Author: Lexi

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  1. Just curious….the dry ingredients do not include “chocolate chips” yet instruction #2 states: “In a bowl combine dry ingredients minus the chocolate chips” Confused?

  2. I cannot wait to try these!!! love love love the almond + coconut flour. . these thumbprint cookies are perfection!! happy holidays!!!