Pumpkin Thumbprint Cookies with Cream Cheese Filling
There’s something about pumpkin cookies that instantly makes it feel like fall. Add a sweet cream cheese center and a sprinkle of pumpkin pie spice, and you have a cookie that was practically made for cozy autumn afternoons.
These Pumpkin Thumbprint Cookies are soft, warmly spiced, and filled with a rich cream cheese frosting. They have all the flavors you expect from a classic pumpkin dessert but in an adorable little cookie that’s easy to serve and share.
They’re perfect for fall baking, Halloween parties, Thanksgiving dessert trays, cookie exchanges, or simply enjoying with a cup of coffee on a chilly afternoon.
Why You’ll Love These Pumpkin Thumbprint Cookies
If you love pumpkin and cream cheese together, these cookies are a must-try. The pumpkin keeps the cookies wonderfully soft while pumpkin pie spice gives them that classic fall flavor.
You’ll also love that they’re:
- Soft and chewy
- Full of real pumpkin
- Easy to make
- Filled with homemade cream cheese frosting
- Perfect for Thanksgiving
- Great for fall cookie trays
- Easy to make ahead
- Absolutely adorable on a dessert table
And unlike traditional thumbprint cookies that are often filled with jam, these get a creamy cheesecake-inspired center.
Ingredients for Pumpkin Thumbprint Cookies
Pumpkin Cookies
You’ll need:
- 2½ cups all-purpose flour
- 1 teaspoon pumpkin pie spice
- 1 teaspoon baking soda
- ½ teaspoon kosher salt
- ¼ teaspoon baking powder
- 1 cup unsalted sweet cream butter, softened
- ⅔ cup packed light brown sugar
- ⅓ cup granulated sugar
- 1 large egg
- 1 teaspoon pure vanilla extract
- 1 cup pumpkin puree
Cream Cheese Filling
You’ll need:
- 4 tablespoons unsalted sweet cream butter, softened
- 4 ounces cream cheese, softened
- 2 cups powdered sugar
- 1 teaspoon pure vanilla extract
- Pumpkin pie spice, for topping
Equipment
- 2 baking sheets
- Parchment paper
- Mini cookie or ice cream scoop
- Tablespoon
- Disposable piping bag
How to Make Pumpkin Thumbprint Cookies
Step 1: Prepare the Oven
Preheat your oven to 350°F.
Line two large baking sheets with parchment paper and set them aside.
Step 2: Combine the Dry Ingredients
In a medium mixing bowl, whisk together the flour, pumpkin pie spice, baking soda, kosher salt, and baking powder.
Set the dry ingredients aside while you prepare the pumpkin cookie dough.
Step 3: Cream the Butter and Sugars
Add the softened butter, brown sugar, and granulated sugar to a large mixing bowl.
Using a hand mixer or stand mixer, cream the ingredients together until the mixture is light and fluffy.
This usually takes about 2–3 minutes.
Step 4: Add the Wet Ingredients
Beat the egg and vanilla extract into the butter mixture until combined.
Add the pumpkin puree and continue mixing until incorporated.
The mixture may look slightly different from traditional cookie dough because of the moisture in the pumpkin. That’s completely normal.
Step 5: Make the Pumpkin Cookie Dough
Gradually add the dry ingredients to the pumpkin mixture.
Mix just until everything is combined and a soft cookie dough forms.
Avoid overmixing once you’ve added the flour.
Step 6: Scoop the Cookies
Using a mini cookie or ice cream scoop, scoop portions of cookie dough onto your prepared baking sheets.
Leave approximately 2 inches between each cookie to give them room to spread.
Step 7: Partially Bake the Cookies
Place the cookies in your preheated oven and bake for 8 minutes.
Remove the baking sheets from the oven.
Step 8: Create the Thumbprints
While the cookies are still warm, use the back of a tablespoon to gently press an indentation into the center of each cookie.
Be careful not to press completely through the cookie.
Return the cookies to the oven and bake for approximately 7 additional minutes, or until the cookies are set and lightly golden around the edges.
Step 9: Cool
Remove the cookies from the oven.
If any of the indentations puffed up while baking, gently press them down again with the back of your tablespoon while the cookies are still warm.
Allow the cookies to cool on the baking sheets for several minutes before transferring them to a wire cooling rack.
Let the cookies cool completely before adding the cream cheese filling.
How to Make the Cream Cheese Filling
While the pumpkin cookies cool, prepare the cream cheese frosting.
Add the softened butter and cream cheese to a medium mixing bowl.
Beat until smooth and creamy.
Gradually add the powdered sugar and vanilla extract.
Continue beating until the filling is completely smooth and fluffy.
Transfer the cream cheese filling to a disposable piping bag.
You can snip off the end of the piping bag or use a decorative piping tip if you’d like the centers to look extra pretty.
Fill the Pumpkin Thumbprint Cookies
Once your cookies are completely cool, pipe the cream cheese filling into the indentation in the center of each cookie.
Finish with a light sprinkle of pumpkin pie spice.
And that’s it! Your pumpkin thumbprint cookies are ready to enjoy.
Tips for Making the Best Pumpkin Cookies
Use pumpkin puree, not pumpkin pie filling. Canned pumpkin puree is plain pumpkin, while pumpkin pie filling contains added sugar and spices.
Measure the flour carefully. Too much flour can make your cookies dense. Spoon the flour into your measuring cup and level it rather than packing it down.
Don’t overmix the dough. Once the flour goes in, mix only until everything is incorporated.
Make the indentations while the cookies are warm. They’ll be much easier to shape without cracking.
Cool before filling. Cream cheese frosting and warm cookies aren’t a good combination. Your cookies should be completely cool before you pipe in the filling.
Use room-temperature cream cheese and butter. This helps create a smooth filling without lumps.
Can I Make These Cookies Ahead of Time?
Yes! If you’re preparing these for Thanksgiving or a fall party, you can make the cookies ahead of time.
Bake the pumpkin cookies and allow them to cool completely. Store the unfilled cookies in an airtight container.
Prepare the cream cheese filling separately and refrigerate it.
When you’re ready to serve, pipe the filling into the cookies and add the pumpkin pie spice.
This also helps keep the cookies looking their best for a party or holiday dessert table.
How to Store Pumpkin Thumbprint Cookies
Because these cookies contain a cream cheese filling, finished cookies should be refrigerated.
Arrange them in an airtight container, placing parchment or wax paper between layers if necessary.
Store them in the refrigerator for up to 3–4 days.
For the best texture, take the cookies out of the refrigerator about 15 minutes before serving.
Can You Freeze Pumpkin Thumbprint Cookies?
For best results, freeze the cookies before adding the cream cheese filling.
Allow the baked cookies to cool completely and place them in a freezer-safe container with parchment paper between the layers.
Freeze for up to 2–3 months.
When you’re ready to enjoy them, thaw the cookies and add freshly made cream cheese filling.
Perfect for a Fall Cookie Tray
These Pumpkin Thumbprint Cookies with Cream Cheese Filling are a fun change from traditional pumpkin pie and pumpkin bread.
They’re soft, sweet, warmly spiced, and filled with creamy frosting that gives you a little bit of pumpkin-and-cheesecake flavor in every bite.
Serve them for Thanksgiving, make them for a Halloween party, add them to a fall cookie exchange, or bake a batch simply because pumpkin season is finally here.
Just don’t be surprised if the cream cheese-filled centers make these the first cookies to disappear from the dessert table.
Pumpkin Thumbprint Cookies with Cream Cheese Filling
Ingredients
Pumpkin Cookies
You'll need:
- 2½ cups all-purpose flour
- 1 teaspoon pumpkin pie spice
- 1 teaspoon baking soda
- ½ teaspoon kosher salt
- ¼ teaspoon baking powder
- 1 cup unsalted sweet cream butter softened
- ⅔ cup packed light brown sugar
- ⅓ cup granulated sugar
- 1 large egg
- 1 teaspoon pure vanilla extract
- 1 cup pumpkin puree
Cream Cheese Filling
You'll need:
- 4 tablespoons unsalted sweet cream butter softened
- 4 ounces cream cheese softened
- 2 cups powdered sugar
- 1 teaspoon pure vanilla extract
- Pumpkin pie spice for topping
Instructions
Step 1: Prepare the Oven
- Preheat your oven to 350°F.
- Line two large baking sheets with parchment paper and set them aside.
Step 2: Combine the Dry Ingredients
- In a medium mixing bowl, whisk together the flour, pumpkin pie spice, baking soda, kosher salt, and baking powder.
- Set the dry ingredients aside while you prepare the pumpkin cookie dough.
Step 3: Cream the Butter and Sugars
- Add the softened butter, brown sugar, and granulated sugar to a large mixing bowl.
- Using a hand mixer or stand mixer, cream the ingredients together until the mixture is light and fluffy.
- This usually takes about 2–3 minutes.
Step 4: Add the Wet Ingredients
- Beat the egg and vanilla extract into the butter mixture until combined.
- Add the pumpkin puree and continue mixing until incorporated.
- The mixture may look slightly different from traditional cookie dough because of the moisture in the pumpkin. That's completely normal.
Step 5: Make the Pumpkin Cookie Dough
- Gradually add the dry ingredients to the pumpkin mixture.
- Mix just until everything is combined and a soft cookie dough forms.
- Avoid overmixing once you've added the flour.
Step 6: Scoop the Cookies
- Using a mini cookie or ice cream scoop, scoop portions of cookie dough onto your prepared baking sheets.
- Leave approximately 2 inches between each cookie to give them room to spread.
Step 7: Partially Bake the Cookies
- Place the cookies in your preheated oven and bake for 8 minutes.
- Remove the baking sheets from the oven.
Step 8: Create the Thumbprints
- While the cookies are still warm, use the back of a tablespoon to gently press an indentation into the center of each cookie.
- Be careful not to press completely through the cookie.
- Return the cookies to the oven and bake for approximately 7 additional minutes, or until the cookies are set and lightly golden around the edges.
Step 9: Cool
- Remove the cookies from the oven.
- If any of the indentations puffed up while baking, gently press them down again with the back of your tablespoon while the cookies are still warm.
- Allow the cookies to cool on the baking sheets for several minutes before transferring them to a wire cooling rack.
- Let the cookies cool completely before adding the cream cheese filling.
How to Make the Cream Cheese Filling
- While the pumpkin cookies cool, prepare the cream cheese frosting.
- Add the softened butter and cream cheese to a medium mixing bowl.
- Beat until smooth and creamy.
- Gradually add the powdered sugar and vanilla extract.
- Continue beating until the filling is completely smooth and fluffy.
- Transfer the cream cheese filling to a disposable piping bag.
- You can snip off the end of the piping bag or use a decorative piping tip if you'd like the centers to look extra pretty.
- Fill the Pumpkin Thumbprint Cookies
- Once your cookies are completely cool, pipe the cream cheese filling into the indentation in the center of each cookie.
- Finish with a light sprinkle of pumpkin pie spice.
- And that's it! Your pumpkin thumbprint cookies are ready to enjoy.
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