Chocolate Thumbprint Cookies | Vegan + Gluten-Free

Dec 21, 2021

A must-try cookie recipe! I love coming up with twists on classic recipes and this is the perfect healthy twist on our favorite holiday cookies! They are easy to make and take common ingredients found in every healthy foodie's kitchen. Plus, they are made without eggs so the allergy foodies can enjoy them too. 

I also swap cane sugar for coconut sugar in cookies as well as it is lower glycemic, better for the body and planet. 


  • Be sure to melt your vegan butter or coconut oil before creaming together with coconut sugar. This will make for a soft and chewy cookie texture.
  • Depending on your gluten-free flour mix, cookies may be dryer than others. The recipe we provide in our gluten-free baking class is the best by far for making these cookies moist while still holding shape and having texture. If your cookie dough seems to dry because of your flour, add another 1/4 cup of pumpkin puree.

Vegan Chocolate Thumbprint Cookies

Vegan Chocolate Thumbprint Cookies

Yield: 12 Cookies
Prep time: 15 MinCook time: 12 MinInactive time: 35 MinTotal time: 1 H & 2 M
Vegan, Grain-Free, Gluten-Free


Dry Ingredients
  • 1/4 tsp. mineral salt
Wet Ingredients
Chocolate Ganache
  • 1/2 cup water 


  1. In a medium bowl, whisk dry ingredients until well combined. Set aside.
  2. In a food processor or with a hand mixer, cream together butter and coconut sugar until light and fluffy, about 2 minutes. Then add in the applesauce or pumpkin puree, and mix again until combined.
  3. With a spatula to fold the wet ingredients into dry ingredients just until mixed.
  4. Scoop the cookie dough into a 1 1/2 tbsp-sized ice cream scoop on a lined baking sheet.
  5. Place the cookie sheet into the freezer to chill for 15-20 minutes. While the cookie dough is chilling, preheat the oven to 350ºF.
  6. Bake cookies for 12-14 minutes, or until the edges have slightly spread. They should still be slightly soft and 'undercooked'.
  7. Immediately and carefully create the “thumbprint:” Press a measuring spoon into the middle of each cookie gently, creating the thumbprint, bowl shape. Allow the cookies to set for 20 minutes on the baking sheet before attempting to move or fill.
  8. CHOCOLATE GANACHE: Prepare the chocolate ganache by blending all ingredients on high until smooth. Pour into a piping bag or squeeze bottle and squeeze into COMPLETELY COOLED cookies. Let set in the fridge. You will still have enough ganache for 1 more batch of cookies. Store leftover ganache in a squeeze bottle in your pantry (not in the fridge or it will harden and won't pour). Label and use within 2 weeks.
  9. Store leftover cookies in an airtight container in the fridge for up to a week or in the freezer for up to 2 months.

*We provide our favorite gluten and grain-free flour mix in our Gluten-Free Baking Class. You can find more details about this class here. Otherwise, use a store-bought gluten-free baking mix.

Did you make this recipe?
Tag @purejoyacademy on instagram and hashtag it #purejoyacademy

Own your health. It starts on your plate. 

Want more Energy, Vitality & PURE JOY? Embark on your journey to a healthier more vibrant YOU with these easy, delicious whole-food, low-carb, plant-based recipes

Join Our Newsletter!

Subscribe to get our latest low-carb, low-sugar recipes, classes, event dates, and happenings by email.