Paleo Chocolate Thumbprint Cookies

These soft and chewy shortbread cookies are filled with a 2-ingredient chocolate center. These paleo chocolate thumbprint cookies are super easy to make and made grain free and dairy free.

paleo shortbread cookies filled with chocolate

I recently decided that I would take a break from dairy for about three weeks to see if it helps clear up my face. I’ve read lots of articles about how diary can contribute to chin and jaw breakouts in women because of all the hormones they use on the cows. So be prepared for mostly dairy free desserts here for a bit.

I am planning to post a dinner recipe here in the next week or so with like a ton of cheese in it so brace yourselves for that one. That will be a dairy overload but I unfortunately won’t be partaking in it. That’s okay because I still have these paleo chocolate thumbprint cookies! YAY!

These cookies were so simple to make. All you have to do is mix the dry ingredients, then mix the wet ingredients together until a dough forms. Separate into balls. Press the balls down with your thumb to create an indent and then bake, fill and serve!

Here’s what you will need to make these paleo chocolate thumbprint cookies

  • almond flour
  • tapioca flour
  • coconut flour
  • granulated sweetener
  • coconut oil
  • egg
  • sticky syrup
  • vegan chocolate chips
  • almond butter
  • baking soda, salt, vanilla extract
hands grabbing paleo shortbread cookies filled with chocolate

Chocolate lovers unite! I have more delicious chocolate filled recipes that I know you will love and to help you get through this holiday baking season! Like this Dark Chocolate Cream Pie with Torched Meringue made gluten free or this Healthy Chocolate Marble Banana Bread!

Paleo Chocolate Thumbprint Cookies

These paleo chocolate thumbprint make a perfect soft and chewy cookie that’s also gluten free and dairy free.
Pin Recipe
Prep Time15 minutes
Cook Time10 minutes
Total Time25 minutes
Course: Dessert, Snack
Keyword: cookies, dairy free, gluten free, paleo
Servings: 12
Author: Ciarra Siller


  • 1 cup almond flour
  • 1/4 cup tapioca flour
  • 1/4 cup coconut flour
  • 3 tbsp granulated sweetener Swerve
  • 1/2 tsp baking soda
  • 1/4 tsp sea salt
  • 1/4 cup coconut oil melted
  • 1 egg room temperature
  • 1/4 cup honey or sticky syrup
  • 1 tsp vanilla extract

Chocolate Filling

  • 1/3 cup dairy free or vegan chocolate chips Lily’s
  • 2 tbsp almond butter or nut butter natural


  • Preheat oven to 350 F and prepare a baking sheet with parchment paper. Set aside.
  • In a bowl, whisk together all wet cookie ingredients. In another bowl, whisk together all dry cookie ingredients. Add your wet ingredients to your dry and stir using a fork until a dough forms. Separate the dough into 12 evenly sized balls and place them about an inch apart on the baking sheet. Use your thumb or the back of a cookie scoop to press them down and create an indent. 
  • Bake cookies for 5 minutes, remove and press the indent down again using the back of a cookie scooper. Return to the oven and bake for another 4-5 minutes. Remove and let cool. 
  • Once cooled, melt the chocolate and almond butter together until smooth. Spoon the mixture into the center of each cookie. Let cool at room temperature or if you can’t wait that long, place in the freezer for 5 minutes or until chocolate has set. 

If you love this recipe, be sure to leave a comment here on the blog or reach out to me on Instagram. I love hearing from you and seeing all your creations!

xx Ciarra

paleo shortbread cookies filled with chocolate

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nicole (thespicetrain.com)
nicole (thespicetrain.com)
5 years ago

These look beautiful!

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I'm Ciarra

Welcome to Peanut Butter Plus Chocolate, where I share indulgent dessert recipes. Here you can find healthier versions of your favorite desserts.



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