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Close up of a paleo thumbprint cookie in a hand while others cool on a wire rack in the background.

Paleo Thumbprint Cookies {Gluten Free + Paleo}

  • Author: Nicole
  • Prep Time: 30 minutes
  • Cook Time: 12 minutes
  • Total Time: 42 minutes
  • Yield: 9 cookies 1x
  • Category: Sweet Treats
  • Method: Bake
  • Cuisine: American


These classic paleo thumbprint cookies use a blackberry chia seed jam and are gluten free, dairy free and refined sugar free for a fun and healthy holiday treat!



The Chia Seed Jam:

  • 3/4 cup berries (I used blackberries)
  • 12 Tablespoons raw honey (I recommend local honey whenever it’s available)
  • 1 1/2 teaspoons chia seeds
  • pinch of unrefined sea salt

The Cookies:


Chia Seed Jam:

  1. In a small saucepan heat the berries over medium-high heat until simmering.
  2. Mash the berries with the back of a spoon as they simmer for 5 minutes.
  3. Reduce the heat to medium-low.
  4. To the cooking berries add 2 Tablespoons honey and a pinch of salt, stir to incorporate. Carefully taste (it’s hot!) and add more honey if needed.
  5. Once the jam tastes as sweet as you’d like stir in the chia seeds. Continue stirring while they thicken, for about 5 minutes.
  6. Remove the saucepan from the heat and cool for 5-10 minutes before transferring to a mason jar. If time allows continue cooling on the kitchen counter without a lid for 15 minutes before adding a lid and storing in the refrigerator. (Placing the lid on immediately traps stream and will result in a slightly thinner jam that will still be delicious so no worries either way!)


  1. Preheat oven to 350 degrees F. Then line a baking sheet with parchment paper.
  2. Prepare flax eggs as listed above. While they “gel” assemble all other ingredients.
  3. In a stand mixer (hand mixer or bowl and whisk) combine flax eggs, coconut oil and honey. Mix on medium-low until completely combined.
  4. Add coconut flour, ground cinnamon, baking soda and salt. Mix on medium speed until all is incorporated.
  5. Transfer the mixing bowl with dough to the refrigerator to chill for at least 30 minutes.
  6. Remove the dough and roll into 9 balls. Place dough balls evenly spaced on your baking sheet and press your thumb or the back of a very round spoon into the center of the ball to make a well for the jam. (I used a 1 teaspoon measuring spoon, as pictured.)
  7. Once your “wells” are made you can pat/pinch the edges of the cookies together to smooth them out since they will crack a little in the well-making process.
  8. Fill your wells with 1 teaspoon each of the chia seed jam you made earlier that has cooled. (*Or as much as needed to fill your wells if you didn’t use a 1 teaspoon to make your wells.)
  9. Bake for 10-12 minutes until the cookies are slightly golden brown.
  10. Remove the cookies from the oven and let them rest on the baking sheet for 5 minutes before transferring them to a wire rack to finish cooling.
  11. Eat and enjoy!

Keywords: thumbprint cookies, paleo, vegan, gluten free, Christmas,

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