Pumpkin Thumbprint Cookies (Cheesecake Filling)

This post may contain affiliate links. Please read our disclosure policy.

We all want a chewy, pumpkin flavored dessert just in time for fall. These wonderful Pumpkin Thumbprint Cookies are calling your name. These delicious Fall cookies have a cheesecake filling and  are perfect for any occasion. Your friends and family will love to take a bite of this tasty cookie recipe!

Pumpkin Thumbprint Cookies on a serving platter.

Pumpkin Thumbprint Cookies

These amazing Pumpkin Cookies are delicious. This recipe has a delicious cream cheese filling in the middle for that perfect texture and flavor combo of pumpkin and filling. This is a quick and easy recipe that only takes 15 minutes to make, so you will have a great cookie recipe in no time to share with your loved ones.

These pumpkin thumbprint cookies will be perfect as party of a cookie tray for a Thanksgiving. Pair them with Double Chocolate Pumpkin CookiesApple Snickerdoodle Cookies and Zucchini Cookies with Cream Cheese Frosting.


  • Flour- You will want to use All-purpose flour for the best results.
  • Pumpkin pie spice- This will give your cookies that pumpkin flavor.
  • Baking soda– This will help your cookies rise in the oven.
  • Salt– The salt will bring out the flavors in the cookies.
  • Baking powder- This will help your ingredients double in size.
  • Butter- You will need to use unsalted to control the amount of salt in a recipe.
  • Light brown sugar- This sugar will add moisture to your cookies.
  • Sugar- Every great dessert has sugar in it.
  • Egg- You need to use eggs at room temperature.
  • Vanilla extract- Use pure vanilla for the best flavoring.
  • Pumpkin puree– You will need to use puree and not the pie filling.
  • Homemade Cream Cheese Frosting Recipe

How to Make Pumpkin Thumbprint Cookies

You want to set your oven to 350 degrees and use parchment paper to line 2 baking sheets.

Add your flour, pumpkin spice, salt, baking powder, and baking soda to a medium sized bowl and whisk until combined.

Beat together the butter and sugars in a large bowl until light and fluffy.

Add in the egg and vanilla and beat again to mix.

Add in the pumpkin and beat.

Pour the dry ingredients into the wet and mix until combined.

Scoop the dough onto the prepared sheets using a mini ice cream scooper.

Put in the oven and bake for 8 minutes.

Make an indent into the center of the cookies with a tablespoon.

Then, place back into the oven for an additional 7 minutes or until light brown.

If you notice the indents in the center puffing up, use the tablespoon again to press down.

Let your cookies sit to cool thoroughly.

Filling directions

Add the butter with the cream cheese, powdered sugar and vanilla in a medium sized bowl and beat until smooth and combined.

Use a scooper to add the frosting into the piping bag and place the frosting into the cooled cookies.

Use some more of the pumpkin spice and sprinkle on top of the finished cookies.

Pumpkin Thumbprint Cookies on a plate with more cookies behind it.

What Candies Can Go in the Thumbprint?

There are many different candies you can use for different recipes. However, for this Pumpkin Thumbprint cookie, you will want candies to compliment the pumpkin flavor. You can add candies like toffee, caramel, or chocolate.

Tips for Storing Thumbprint Cookies

You want your Thumbprint cookies to last. The best thing to store these cookies is in an airtight container. These will need to be placed in the fridge because this recipe had a cream cheese filling. You can also place them in a freezer bag.

Pumpkin Thumbprint Cookies on a cloth with leaves behind it.

More Cookie Recipes

Pumpkin Thumbprint Cookies

We all want a chewy, pumpkin flavored dessert just in time for fall. These wonderful Pumpkin Thumbprint Cookies are calling your name. These cookies are perfect for any occasion and may become a new favorite flavor of cookie. Your friends and family will love to take a bite of this tasty cookie recipe!
Servings: 25
Prep: 15 mins
Cook: 15 mins
Total: 30 mins


  • 2 ½ C flour
  • 1 tsp. pumpkin pie spice
  • 1 tsp. baking soda
  • 1/2 tsp. kosher salt
  • 1/4 tsp. baking powder
  • 1 C Unsalted butter softened
  • 2/3 C packed light brown sugar
  • 1/3 C sugar
  • 1 large egg
  • 1 tsp pure vanilla extract
  • 1 C pumpkin puree

Cream Cheese filling :

  • 4 tbsp. Unsalted butter softened
  • 4 oz. cream cheese softened
  • 2 c. powdered sugar
  • 1 tsp. pure vanilla extract
  • Pumpkin pie spice for topping


  • Preheat the oven to 350 and line two baking sheets with parchment
  • Using a medium bowl, whisk flour, pumpkin pie spice, baking soda, salt, and baking powder until combined.
  • In a large bowl, cream butter and sugars until light and fluffy.
  • Beat in egg and vanilla.
  • Beat in pumpkin.
  • Add dry ingredients to the wet and beat until combined
  • Using a mini ice cream scooper, scoop some dough onto the cookie tray
  • Bake for 8 minutes
  • Using a tablespoon make a indent into the cookies
  • Place back into the oven for 7 more minutes or until golden brown
  • If the indents puffed up, use the tablespoon and press the indent back down
  • Allow the cookies to cool completely

Filling directions

  • Using a medium bowl, beat butter with cream cheese, powdered sugar, and vanilla until combined and smooth
  • Scoop the frosting into the piping bag and pipe into cooled cookies.
  • Sprinkle with pumpkin spice on top


Pumpkin Thumbprint Cookies with Cream Cheese Filling


Leave a Review!

We LOVE hearing from you! Submit your question or comment here.

Your email address will not be published.

Your email address will not be published. Required fields are marked *

Recipe Rating:

I accept the Privacy Policy

Scroll to Top