Hello, dear friends, I’m so excited you’re here! Pumpkin Cheesecake Thumbprint Cookies are my go-to autumn delight, and I simply can’t wait to share this cozy, heartwarming recipe with you. Imagine soft, spiced pumpkin cookie dough, gently indented and filled with creamy, tangy cheesecake… sweet, seasonal comfort in every bite.
These cookies feel like a warm hug, perfect for chilly mornings, evening tea, or spontaneous snack moments. Let’s dive in together!
WHY MAKE THIS RECIPE
You might be thinking, “Another pumpkin cookie recipe? What makes this one so special?” Well, let me tell you! First off, it’s incredibly quick. We’re talking minimal effort for maximum reward here. With just a handful of ingredients, you can transform simple pantry staples into a delightful treat that tastes like you spent hours slaving away. Secondly, the combination of a soft, spiced pumpkin cookie base with a creamy, tangy cheesecake filling is simply divine. It’s the perfect balance of sweet and savory, with a delightful texture contrast that will keep you coming back for more.
Plus, these cookies are perfect for any occasion: a cozy night in, a potluck with friends, or a festive holiday gathering. They’re a crowd-pleaser that everyone will adore!
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PUMPKIN CHEESECAKE THUMBPRINT COOKIES
- Total Time: 34 minutes
- Yield: 24 cookies 1x
- Diet: Vegetarian
Description
Soft spiced pumpkin cookies with a creamy cheesecake filling in the center — the perfect fall-inspired thumbprint treat.
Ingredients
For the cookies:
1/2 cup unsalted butter, softened
1/2 cup granulated sugar
1/2 cup brown sugar
1/2 cup pumpkin purée
1 large egg yolk
1 teaspoon vanilla extract
1 3/4 cups all-purpose flour
1 teaspoon baking powder
1/2 teaspoon baking soda
1 teaspoon cinnamon
1/2 teaspoon nutmeg
1/4 teaspoon cloves
1/2 teaspoon salt
For the cheesecake filling:
6 oz cream cheese, softened
1/4 cup powdered sugar
1/2 teaspoon vanilla extract
Instructions
1. Preheat oven to 350°F (175°C). Line baking sheets with parchment paper.
2. In a large bowl, cream together butter, granulated sugar, and brown sugar until light and fluffy.
3. Mix in pumpkin purée, egg yolk, and vanilla extract until smooth.
4. In a separate bowl, whisk together flour, baking powder, baking soda, cinnamon, nutmeg, cloves, and salt.
5. Gradually add dry ingredients into wet mixture until just combined.
6. In a small bowl, beat cream cheese, powdered sugar, and vanilla until smooth to make the filling.
7. Scoop tablespoon-sized portions of dough, roll into balls, and place on baking sheet. Use your thumb or a spoon to create an indentation in each cookie.
8. Pipe or spoon cheesecake filling into the indentations.
9. Bake for 12–14 minutes, until cookies are set and slightly golden at the edges.
10. Cool completely on a wire rack before serving.
Notes
Chill dough for 20–30 minutes if it feels too sticky to roll.
You can sprinkle a little cinnamon sugar on top of the filling before baking for extra flavor.
Store cookies in the refrigerator for freshness, as they contain a cream cheese filling.
- Prep Time: 20 minutes
- Cook Time: 14 minutes
- Category: Dessert
- Method: Baking
- Cuisine: American
Nutrition
- Serving Size: 1 cookie
- Calories: 150
- Sugar: 11g
- Sodium: 120mg
- Fat: 7g
- Saturated Fat: 4g
- Unsaturated Fat: 2g
- Trans Fat: 0g
- Carbohydrates: 20g
- Fiber: 1g
- Protein: 2g
- Cholesterol: 30mg
Keywords: pumpkin cheesecake, thumbprint cookies, fall dessert, spiced cookies
HOW TO MAKE PUMPKIN CHEESECAKE THUMBPRINT COOKIES
INGREDIENTS:
- 1 cup (2 sticks) unsalted butter, softened
- 1 cup granulated sugar
- 1 large egg
- 1 teaspoon vanilla extract
- 1 (15-ounce) can pumpkin puree (not pumpkin pie filling)
- 2 ½ cups all-purpose flour
- 2 teaspoons baking powder
- 1 teaspoon ground cinnamon
- ½ teaspoon ground ginger
- ¼ teaspoon ground nutmeg
- ¼ teaspoon ground cloves
- ½ teaspoon salt
For the Cheesecake Filling:
- 8 ounces cream cheese, softened
- ½ cup powdered sugar
- 1 teaspoon vanilla extract
DIRECTIONS:

- Preheat & Prep: Preheat your oven to 375°F (190°C). Line two baking sheets with parchment paper.
- Cream Butter & Sugar: In a large mixing bowl, cream together the softened butter and granulated sugar until light and fluffy.
- Add Wet Ingredients: Beat in the egg and vanilla extract until well combined. Then, stir in the pumpkin puree until smooth.
- Combine Dry Ingredients: In a separate medium bowl, whisk together the flour, baking powder, cinnamon, ginger, nutmeg, cloves, and salt.
- Combine Wet & Dry: Gradually add the dry ingredients to the wet ingredients, mixing until just combined. Be careful not to overmix!
- Form Cookies: Roll the dough into 1-inch balls and place them about 2 inches apart on the prepared baking sheets.
- Make Thumbprints: Using your thumb or the back of a round teaspoon, gently press an indentation into the center of each cookie ball.
- Bake: Bake for 10-12 minutes, or until the edges are lightly golden and the cookies are set.
- Cool: Remove from the oven and let cool on the baking sheets for a few minutes before transferring them to a wire rack to cool completely.
- Make Cheesecake Filling: While the cookies are cooling, prepare the filling. In a small bowl, beat the softened cream cheese, powdered sugar, and vanilla extract together until smooth and creamy.
- Fill & Enjoy: Once the cookies are completely cool, spoon or pipe the cheesecake filling into the thumbprint indentations. Serve immediately or chill for a firmer filling.

HOW TO SERVE PUMPKIN CHEESECAKE THUMBPRINT COOKIES
These delightful cookies are incredibly versatile! They’re perfect as a standalone treat with a warm cup of coffee or tea, especially on a chilly autumn afternoon. Imagine curling up with a good book, a cozy blanket, and a plate of these little beauties, pure bliss! They also make a fantastic addition to any dessert spread, from casual gatherings to holiday feasts.
Their vibrant color and inviting aroma will draw everyone in. You can even drizzle a little caramel sauce over them for an extra touch of decadence, or sprinkle a tiny pinch of cinnamon on top of the cheesecake filling for an elegant finish.
HOW TO STORE PUMPKIN CHEESECAKE THUMBPRINT COOKIES
Because of the cream cheese filling, these cookies are best stored in an airtight container in the refrigerator. They will stay fresh for up to 3-4 days. If you’re planning to make them ahead of time for a party, you can bake the cookies, let them cool completely, and store them at room temperature for a day or two. Then, prepare the filling and fill the cookies just before serving.
You can also freeze the baked, unfilled cookies for up to 2 months. Just thaw them at room temperature, then fill and serve.

TIPS TO MAKE PUMPKIN CHEESECAKE THUMBPRINT COOKIES
TIPS AND NOTES: YOUR KITCHEN COMPANION
- Don’t Overmix: When combining the wet and dry ingredients, mix just until no dry streaks remain. Overmixing can lead to tough cookies!
- Room Temperature Ingredients: Ensure your butter and cream cheese are truly softened to room temperature. This makes for a smoother, more even mixture and prevents lumps.
- Pumpkin Puree vs. Pie Filling: Make sure you’re using plain pumpkin puree, not pumpkin pie filling, which already has spices and sugar added.
- Chill the Dough (Optional): If your dough feels a bit too sticky to roll, you can chill it in the refrigerator for 20-30 minutes. This will make it easier to handle.
- Deep Thumbprints: Don’t be shy with your thumbprints! Make them deep enough to hold a good amount of the delicious cheesecake filling. If they puff up too much during baking, you can gently re-press them immediately after taking them out of the oven.
- Cool Completely: It’s crucial that the cookies are completely cool before you add the cheesecake filling. Otherwise, the warmth will melt the cream cheese, and you’ll have a runny mess.
- Piping vs. Spooning: For a neater look, you can pipe the cheesecake filling into the thumbprints using a piping bag with a round tip (or even a Ziploc bag with a corner snipped off). Spooning works just as well for a more rustic charm!
DETAILS
These Pumpkin Cheesecake Thumbprint Cookies are a delightful fusion of classic fall flavors. The soft, cake-like pumpkin cookie is generously spiced with cinnamon, ginger, nutmeg, and cloves, bringing all the warm, aromatic notes of autumn to your palate. The subtle sweetness of the cookie is perfectly complemented by the creamy, slightly tart cheesecake filling, creating a harmonious balance that is truly addictive. They’re substantial enough to feel like a proper treat but light enough that you’ll be tempted to have more than one!
VARIATION
- Spiced Crumble Topping: For an extra layer of texture and flavor, sprinkle a little streusel crumble (made with flour, brown sugar, and butter) over the cheesecake filling before serving.
- Chocolate Drizzle: A drizzle of melted dark or white chocolate over the finished cookies would add a lovely touch of elegance and a different flavor profile.
- Nutty Twist: Finely chopped pecans or walnuts can be mixed into the cookie dough for a delightful crunch.
- Different Spices: Feel free to adjust the spice blend to your liking. A pinch of allspice or cardamom could add an interesting twist.
- Maple Glaze: Instead of cheesecake filling, you could opt for a simple maple glaze drizzled over the cooled cookies for a different kind of sweetness.
NOTES
These cookies are surprisingly easy and a fantastic recipe to get kids involved in the kitchen (especially the thumbprint part!). They are also incredibly adaptable, so don’t be afraid to experiment with your favorite fall flavors. Remember, the key to success is to use good quality ingredients and not to overmix the dough. Enjoy the process and savor the delicious results!

FAQS
Can I use canned pumpkin pie filling instead of pumpkin puree?
No, it’s very important to use plain pumpkin puree. Pumpkin pie filling already contains spices and sweeteners, and using it will significantly alter the taste and texture of your cookies.
My cookies spread too much! What went wrong?
This could be due to several factors. Ensure your butter wasn’t too soft (almost melted). Also, make sure your oven temperature is accurate. Sometimes, chilling the dough for 20-30 minutes before rolling can help prevent excessive spreading.
Can I make these gluten-free?
While I haven’t personally tested it, you could try substituting the all-purpose flour with a 1:1 gluten-free baking flour blend. Results may vary slightly in texture.
Can I make the cookie dough ahead of time?
Yes! You can prepare the cookie dough and store it in an airtight container in the refrigerator for up to 2-3 days. When ready to bake, let it come to room temperature slightly before rolling and baking.
How do I get neat-looking thumbprints?
For perfectly round indentations, you can use the back of a rounded measuring spoon (like a teaspoon or half-teaspoon) instead of your thumb. If the cookies puff up too much during baking, gently re-press the indentations with the back of the spoon immediately after removing them from the oven.
CONCLUSION
And there you have it, friends! A simple, irresistible recipe for Pumpkin Cheesecake Thumbprint Cookies that will undoubtedly become a staple in your autumn baking repertoire. The combination of tender, spiced pumpkin and creamy, tangy cheesecake is truly a match made in heaven. These cookies are more than just a sweet treat; they’re a little bite of fall, a moment of comfort, and a perfect excuse to gather with loved ones. So, go ahead, bake a batch, share them with someone special, and let the cozy vibes of the season fill your home. Happy baking!