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Pumpkin Pie Thumbprint Cookies

  • Author: Maggie Michalczyk, RDN
  • Prep Time: 5 minutes
  • Cook Time: 11 minutes
  • Total Time: 16 minutes
  • Yield: 18 cookies 1x
  • Category: pumpkin recipes
  • Method: bake
  • Cuisine: american


Pumpkin pie thumbprint cookies are a cross between a cookie and a slice of pumpkin pie! Soft pumpkin cookies topped with a cream cheese filling with pecan pieces and pumpkin spice on top, they make for the perfect treat or dessert!


  • 1 cup whole-wheat pastry flour
  • 2 tsp. pumpkin pie spice
  • 1/2 tsp. baking powder
  • 1/2 tsp. baking soda
  • 1/4 tsp. plus a pinch of salt
  • 1/2 cup packed light brown sugar or coconut sugar
  • 1/2 cup pumpkin puree
  • 1/3 cup coconut oil
  • 1 large egg
  • 1 tsp.vanilla extract
  • 4 ounces cream cheese, at room temperature
  • 2 tbsp. unsalted butter, at room temperature
  • 1/2 cup confectioners’ sugar
  • 1/2 tsp. fresh lemon juice
  • dash of pumpkin pie spice
  • 1/4 cup pecan pieces 


  1. Preheat the oven to 375 degrees F. Line a baking sheet with parchment paper. 
  2. In a small bowl, whisk together whole-wheat pastry flour, pumpkin pie spice, baking powder, baking soda, and sat. 
  3. In another medium bowl, combine brown sugar, pumpkin puree, coconut oil, egg, and vanilla, Mix with a wooden spoon until combined. Add the dry ingredients to the wet and mix with a wooden spoon until combined.
  4. Use a cookie scoop to portion out cookie dough on the cookie sheet. I recommend filling the cookie scoop about halfway full as the portion size, because the cookies will spread. 1/2 of a cookie scoop makes for a typical cookie size.
  5. Bake for 10-11 minutes. Remove the cookies from oven, and use your thumb to gently make a small indentation for the thumbprint. Let cool.  
  6. While the cookies are cooling, make the cream cheese frosting. Use a stand or a hand mixer to beat together softened cream cheese, butter, confectioners’ sugar and pinch of salt and pumpkin pie spice. 
  7. Once the cookies are mostly cooled pipe* the cream cheese frosting onto each cookie and top with pecan pieces and extra pumpkin pie spice. Enjoy! 


*Putting the cream cheese frosting into a plastic bag and cutting the tip off makes for a great pipping bag. 

Keywords: pumpkin thumbprint cookies