delicious pumpkin cookies with apple butter thumbprint on white plates

Pumpkin Cookies with Apple Butter Thumbprint – Paleo, Vegan

  • Author: Beth of A Meal In Mind
  • Prep Time: 15 minutes
  • Cook Time: 15 minutes
  • Total Time: 30 minutes
  • Yield: 12 cookies 1x
  • Category: Dessert, Snack
  • Method: Oven
  • Cuisine: American


These slightly soft pumpkin cookies with apple butter thumbprint and maple drizzle will melt in your mouth. They make it so easy to get a little bit of that pumpkin-pie-spice flavor. Gluten free! Vegan!



For the cookie dough:

  • 1 2/3 cups packed fine almond flour (not almond meal) 
  • ¼ cup organic coconut sugar 
  • ¼ cup coconut flour
  • 1/4 teaspoon baking soda
  • 1 tablespoon pumpkin pie spice (or 1 1/2 teaspoons cinnamon, 1/2 teaspoon nutmeg, 1/2 teaspoon ground ginger, 1/4 teaspoon allspice or ground cloves)
  • 1/4 teaspoon salt
  • 1/4 cup coconut oil (room temperature)
  • 1 flax egg (1 tablespoon ground flax seed + 2 ½ tablespoons water (for a crisper cookie, or at high altitude, use 1 tablespoon water)
  • 1 teaspoon vanilla extract
  • 1/3 cup pumpkin puree
  • 1/3 cup apple butter, for thumbprints (recipe here)

Maple-vanilla drizzle:

  • ¼ cup powdered sugar
  • 2 teaspoons pure maple syrup
  • 2 teaspoons vanilla extract (or for more maple flavor, another teaspoon maple)

Other toppings to consider: 12 pecan halves, candy corn, a sprinkle of cinnamon


  1. Preheat oven to 350 degrees F. Line a large baking sheet with parchment paper and set aside.
  2. Measure almond flour, coconut flour, sugar, baking soda, spices and salt into your food processor. Process until well mixed, just a few pulses.
  3. Drop in the coconut oil and process until mixed in, about 30 seconds. 
  4. Add the pumpkin puree, flax egg and vanilla extract. Process until well combined and the dough gathers up in one area of the food processor bowl. 
  5. Allow dough to sit for 5 minutes for coconut flour to hydrate. The dough should be workable and not too sticky. 
  6. Next divide and roll the dough into 12 balls of about 1 ½-inch across. 
  7. Flatten each dough ball between your hands, keeping the cookies round. Place them on the prepared cookie sheet. To make a thumbprint, press gently with your thumb in the center until the cookies are about 1/4 inch thick in the center and about ½ inch thick on the edges. 
  8. Bake for 12-15 minutes (at high altitude, bake for 15 minutes). 
  9. Remove from oven, transfer to a wire rack and allow cookies to cool completely before spooning a little apple butter into each well. Makes about 12 cookies.
  10. For the drizzle: In a small bowl, mix together the powdered sugar, pure maple syrup and vanilla. If frosting is too thick to drizzle, you can add a teaspoon or two more maple syrup to make it drizzle-able from a spoon. Frost each cookie, then enjoy! Sprinkle top of frosting with a little cinnamon for a gorgeous look. 


Cookies will get softer each day. Cookies can be stored in a container at room temp for a few days, then I recommend storing them in the fridge – if any are left.

Keywords: pumpkin cookies, apple butter filling, thumbprint cookie, maple drizzle, easy recipe, gluten free, vegan, paleo