If you are looking for a delightful autumn treat that combines the warm spices of fall with a creamy, dreamy center, you have to try this Pumpkin Cheesecake Thumbprint Cookies Recipe. These cookies bring together the buttery softness of a classic thumbprint cookie with a luscious pumpkin cheesecake filling that’s perfectly spiced and sweet. Every bite offers a tender crumb that melts in your mouth, balanced by the tangy pumpkin cream cheese and a subtle dusting of powdered sugar that gives these cookies their irresistible charm. Whether you’re baking for a holiday gathering or just want to cozy up with a comforting snack, this Pumpkin Cheesecake Thumbprint Cookies Recipe will become your new favorite go-to dessert.

Ingredients You’ll Need
The ingredients for this recipe are simple yet crucial to nailing the perfect texture and flavor balance in the cookies. Each component plays a key role: the butter and sugar create a tender crumb, while the pumpkin puree and cream cheese filling bring that signature moist, flavorful center.
- Unsalted butter: 1 cup (2 sticks) at room temperature for a creamy, rich dough base.
- Granulated sugar: 1/2 cup to add sweetness and help the cookies brown just right.
- Vanilla extract: 1 teaspoon to enhance all the warm, comforting flavors.
- All-purpose flour: 2 cups to give structure without making the cookies tough.
- Salt: 1/4 teaspoon to balance the sweetness and enhance taste.
- Cream cheese: 4 ounces at room temperature to create the silky cheesecake filling.
- Canned pumpkin puree: 1/4 cup to infuse the filling with rich pumpkin flavor and moisture.
- Powdered sugar: 1/4 cup for sweetness in the filling and additional for dusting if desired.
- Pumpkin pie spice: 1/2 teaspoon to provide that classic fall spice blend without overpowering.
How to Make Pumpkin Cheesecake Thumbprint Cookies Recipe
Step 1: Prepare Your Baking Area
Start by preheating your oven to 350°F (175°C) and lining a baking sheet with parchment paper. This simple prep ensures you get perfectly baked cookies without sticking or burning, setting you up for success from the very start.
Step 2: Cream Butter and Sugar
In a large mixing bowl, use an electric mixer to beat the butter and granulated sugar together until the mixture is light, fluffy, and pale in color. This step is essential for giving your cookies a tender, melt-in-your-mouth texture, so don’t rush it.
Step 3: Mix in Vanilla
Add the vanilla extract and mix it well into the creamed butter and sugar. The vanilla will help round out the flavors and marry the buttery dough with the pumpkin filling beautifully.
Step 4: Add Dry Ingredients
Gradually fold in the flour and salt. Mix just until the dough comes together; overmixing can lead to tougher cookies, so stop once you see a soft yet manageable dough forming.
Step 5: Shape the Dough
Roll the dough into 1-inch balls and place them about 2 inches apart on your prepared baking sheet. The perfect spacing lets the cookies spread slightly without sticking to each other.
Step 6: Create the Thumbprint Indentation
Gently press your thumb or the back of a teaspoon in the center of each dough ball to create an indentation. Be careful not to press all the way through—the aim is to create a little well for the pumpkin cheesecake filling.
Step 7: Make the Pumpkin Cheesecake Filling
In a separate bowl, beat together the cream cheese, pumpkin puree, powdered sugar, and pumpkin pie spice until smooth and evenly combined. This luscious filling is the heart of this Pumpkin Cheesecake Thumbprint Cookies Recipe, adding creaminess and festive flavor to every bite.
Step 8: Fill the Cookies
Carefully spoon about 1/2 teaspoon of the pumpkin cheesecake mixture into the indentation on each cookie ball. Don’t overfill or the filling might overflow during baking, but don’t be shy—you want that creamy center!
Step 9: Bake the Cookies
Bake the cookies for 12 to 15 minutes, or until the edges are lightly golden and the filling looks set. The smell during this step is pure cozy autumn magic.
Step 10: Cool the Cookies
Once out of the oven, let the cookies cool on the baking sheet for 5 minutes before carefully transferring them to a wire rack to cool completely. This helps them firm up nicely and prevents the filling from getting messy.
Step 11: Add the Finishing Touch
After the cookies have cooled, dust them with a little extra powdered sugar if you want to add a subtle sweetness and an elegant finish. This final step makes these cookies even more irresistible.
How to Serve Pumpkin Cheesecake Thumbprint Cookies Recipe

Garnishes
Sprinkle additional pumpkin pie spice or finely chopped toasted pecans on top to add a dash of texture and spice that complements the pumpkin cheesecake center wonderfully. A drizzle of caramel sauce can also elevate these cookies to dessert-table stardom.
Side Dishes
Your Pumpkin Cheesecake Thumbprint Cookies Recipe pairs beautifully with a steaming cup of chai tea, hot coffee, or a glass of cold milk. These beverages highlight the spices and richness while balancing the creamy cheesecake filling.
Creative Ways to Present
For a festive look, arrange the cookies on a platter with seasonal garnishes like cinnamon sticks, star anise, or mini pumpkins. You can also stack them in a pretty tin or wrap in cellophane tied with a ribbon for an adorable gift or party favor.
Make Ahead and Storage
Storing Leftovers
Keep any leftover cookies in an airtight container at room temperature for up to three days. This keeps the cookies tender and the filling fresh, perfect for enjoying over a few days without losing that fresh-baked magic.
Freezing
You can freeze baked Pumpkin Cheesecake Thumbprint Cookies by placing them in a single layer on a baking sheet and freezing until solid, then transferring to a freezer-safe container or bag. They freeze beautifully for up to two months and thaw quickly at room temperature.
Reheating
To refresh the cookies after freezing, warm them gently in a 300°F oven for 5-7 minutes. This revives that soft texture and creamy filling without drying them out—just like freshly baked.
FAQs
Can I substitute fresh pumpkin for canned pumpkin puree?
While fresh pumpkin can be used, you’ll need to cook and puree it first to remove excess moisture and concentrate the flavor. Canned pumpkin puree is recommended for consistent texture and taste in this Pumpkin Cheesecake Thumbprint Cookies Recipe.
Is cream cheese necessary for the filling?
Yes, cream cheese is key to achieving the smooth, rich cheesecake filling that defines this recipe. It balances the sweetness and gives the cookies their signature creamy center.
Can I make these vegan or dairy-free?
You can try substituting vegan butter and cream cheese alternatives, but results may vary in texture and flavor. The classic version of the Pumpkin Cheesecake Thumbprint Cookies Recipe shines brightest with real butter and cream cheese.
How do I prevent the filling from overflowing during baking?
Use small spoonfuls (about 1/2 teaspoon) of filling and press only gently when making the indentation. This prevents the filling from spilling out and keeps the cookies looking neat and inviting.
What if I don’t have pumpkin pie spice?
You can make your own blend using cinnamon, nutmeg, ginger, and cloves in small amounts. This mix will capture the warm, spicy notes essential to the Pumpkin Cheesecake Thumbprint Cookies Recipe.
Final Thoughts
There is something incredibly satisfying about baking these Pumpkin Cheesecake Thumbprint Cookies Recipe, especially when the smell of spices and pumpkin fills your kitchen. They are truly a crowd-pleaser and a perfect way to share cozy fall flavors with friends and family. Trust me, once you try them, this recipe will become a beloved staple you’ll return to every autumn season. Happy baking!
Print
Pumpkin Cheesecake Thumbprint Cookies Recipe
- Prep Time: 20 minutes
- Cook Time: 15 minutes
- Total Time: 35 minutes
- Yield: Approximately 24 cookies
- Category: Dessert, Snack
- Method: Baking
- Cuisine: American
- Diet: Vegetarian
Description
These Pumpkin Cheesecake Thumbprint Cookies combine a tender, buttery cookie base with a creamy pumpkin cheesecake filling, infused with warm pumpkin pie spice. Perfect for fall celebrations or anytime you crave a seasonal treat, these cookies are easy to make and deliciously festive.
Ingredients
Cookie Dough
- 1 cup (2 sticks) unsalted butter, at room temperature
- 1/2 cup granulated sugar
- 1 teaspoon vanilla extract
- 2 cups all-purpose flour
- 1/4 teaspoon salt
Pumpkin Cheesecake Filling
- 4 ounces cream cheese, at room temperature
- 1/4 cup canned pumpkin puree
- 1/4 cup powdered sugar
- 1/2 teaspoon pumpkin pie spice
Optional
- Additional powdered sugar for dusting
Instructions
- Preheat Oven: Preheat your oven to 350°F (175°C) and line a baking sheet with parchment paper to prepare for baking.
- Cream Butter and Sugar: In a large mixing bowl, use an electric mixer to cream the butter and granulated sugar together until the mixture is light, fluffy, and well combined, about 2-3 minutes.
- Add Vanilla: Mix in the vanilla extract thoroughly to incorporate flavor.
- Mix Dry Ingredients: Gradually add the all-purpose flour and salt to the butter mixture, stirring gently until the dough just comes together. Avoid overmixing to keep the cookies tender.
- Form Dough Balls: Roll the dough into 1-inch balls and arrange them evenly on the prepared baking sheet, spacing each about 2 inches apart to allow for slight spreading.
- Create Thumbprints: Press a gentle indentation into the center of each dough ball using your thumb or the back of a teaspoon, being careful not to press through the dough.
- Prepare Filling: In a separate bowl, beat together the room-temperature cream cheese, pumpkin puree, powdered sugar, and pumpkin pie spice until the filling is smooth and creamy.
- Fill the Cookies: Spoon about 1/2 teaspoon of the pumpkin cheesecake mixture into each indentation on the dough balls.
- Bake: Place the baking sheet in the preheated oven and bake the cookies for 12-15 minutes, or until the edges turn lightly golden brown.
- Cool: Remove the cookies from the oven and let them cool on the baking sheet for 5 minutes before transferring them to a wire rack to cool completely.
- Optional Dusting: Once cooled, dust the cookies with additional powdered sugar, if desired, for a festive finishing touch.
Notes
- Ensure the butter and cream cheese are at room temperature for easier mixing and a smoother texture.
- Do not overmix the dough to keep the cookies tender and crumbly.
- Spacing the cookies properly helps prevent them from merging during baking.
- Store the cookies in an airtight container at room temperature for up to 3 days or refrigerate to extend freshness.
- Optional powdered sugar gives a nice aesthetic touch but can be omitted for less sweetness.

