These pumpkin cheesecake cookies are soft pumpkin spice cookies with a well in the middle, filled with a sweet, tangy cream cheese filling once they have cooled. One batch makes 18 to 20 cookies, and they are ready in about an hour and a half, most of it chilling time.
The trick is that the cheesecake never goes into the oven. Bake the cookies with a shallow dip in each center, let them cool, then pipe in the chilled filling. No leaking, no puffed rubbery tops, and the cookies hold their shape in the fridge for days.
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- Makes: about 18 to 20 cookies, 2 tablespoons of dough each
- Bake: 350°F (175°C) for 12 to 14 minutes
- Chill: 30 minutes for the dough and the filling, 20 minutes after filling
- Filling: 8 ounces cream cheese, ¼ cup sugar, vanilla, and an optional spoon of heat-treated flour
- Pumpkin: ¾ cup canned pumpkin puree, never pumpkin pie filling
- Storage: airtight in the fridge for up to 4 days
Filled, Not Stuffed: Why the Cheesecake Goes in Last
Many recipes for cheesecake stuffed pumpkin cookies wrap a ball of cream cheese inside the dough and bake it. I tried baking the filling in the cookie, and the result was leaking, puffed tops and a rubbery center. Cream cheese filling without an egg is not meant to bake.
Piping it in after baking solves all of that. The cookie stays soft and cakey, the filling stays creamy and cool, and you get a clear contrast between warm spice and tang. It tastes like a bite of pumpkin cheesecake in a cookie you can pick up.
Mix the Cream Cheese Filling First
Beat the softened cream cheese until there are no lumps, then add the sugar, vanilla, and flour if using. The flour is optional and only makes the filling slightly firmer. Since the filling is not baked, heat-treat the flour first: microwave it for 1 minute, stirring halfway, or bake it at 300°F for 5 to 7 minutes, then let it cool.
Spoon the filling into a piping bag or a zip-top bag with one corner snipped off and chill it for at least 30 minutes. Making it first means it is firm and ready by the time the cookies have cooled. If you like this filling, it is close to my cream cheese filling for cakes.
The Pumpkin Cookie Dough
Cream the softened butter with the brown sugar and granulated sugar for 2 to 3 minutes, until pale and fluffy. Butter that is too cold will not cream, and melted butter makes the cookies spread. Beat in the pumpkin puree, egg, and vanilla.
Whisk the flour, baking soda, baking powder, salt, pumpkin pie spice, and cinnamon in a second bowl, then add them to the wet mix a little at a time. The dough will be soft and thick.
Cover it and chill for 30 minutes. Pumpkin adds a lot of moisture, and without this rest the cookies spread flat and lose the well you need for the filling. I also tested the dough with oil in place of butter. The cookies were softer but too weak to hold the cheesecake center, so butter it is.
Shaping the Wells and Baking
Heat the oven to 350°F and line two baking sheets with parchment. Scoop about 2 tablespoons of dough per cookie, roll into balls, and space them 2 inches apart. Flatten each one a little, then press a shallow well into the center with your thumb or the back of a measuring spoon.
Bake for 12 to 14 minutes, until the edges are set and the tops look just done. The centers puff up in the oven, which is normal. While the cookies are still warm, press the wells down again, then let them sit on the sheet for 5 minutes before moving them to a rack to cool completely.
Piping In the Cheesecake
Only fill fully cooled cookies. Even a little warmth melts the cream cheese and it runs over the edges. Pipe 1 to 1½ teaspoons of filling into each well, using a small star tip for a swirl or a plain snipped bag for a smooth top. Chill the filled cookies for 20 minutes so the filling sets, then serve.
Serve them cold for a firm, clean bite, or let them sit 5 to 10 minutes at room temperature for a softer cookie and a brighter cream cheese flavor.
Flat Cookies, Runny Filling, and Other Fixes
- Cookies spread flat: the dough was not chilled, or the butter was too soft. Chill the full 30 minutes and keep the second tray in the fridge while the first bakes.
- No room for the filling: the wells puffed closed. Press them again right after baking, while the cookies are warm.
- Filling runs off: the cookies were still warm, or the filling was not chilled. Cool completely and chill the filled cookies 20 minutes.
- Lumpy filling: the cream cheese was cold. Let it soften fully and beat it alone before adding the sugar.
- Cookies taste bland: pumpkin pie filling was used instead of plain puree, or the spices are old.
Storing and Baking Ahead
Because of the cream cheese, keep the filled cookies in an airtight container in the fridge for up to 4 days, in a single layer or with parchment between layers. For a party or Thanksgiving, bake the cookies a day ahead, store them airtight, and pipe in the filling on the day you serve them. They look freshest that way.
More Pumpkin Bakes for the Same Tray
For a fall cookie platter, pair these with pumpkin pie cookies, pumpkin snickerdoodles, and pumpkin spice thumbprint cookies. If you love the cheesecake side most, try mini pumpkin cheesecakes, pumpkin pie cheesecake, or the oven-free no bake pumpkin cheesecake balls. For a dessert table that feeds a crowd, pumpkin squares come out of one 9×13 pan.
Pumpkin Cheesecake Cookie Questions
Can I use pumpkin pie filling instead of puree?
No. Pumpkin pie filling already has sugar and spices, so the cookies turn too sweet and spread. Use plain canned pumpkin puree.
Do pumpkin cheesecake cookies need to be refrigerated?
Yes. The cream cheese filling is not baked, so keep the cookies in the fridge and serve them within 4 days.
Can I freeze them?
Freeze the baked, unfilled cookies in an airtight container, thaw them at room temperature, then pipe in freshly made filling.
Why put flour in the cheesecake filling?
It is optional and makes the filling a little firmer so it holds a piped swirl. Heat-treat it first, since the filling is never baked.
Save These for Fall Baking
Pin these pumpkin cheesecake cookies to your fall or Thanksgiving dessert board so the recipe is there when pumpkin season starts. If you bake them, tell me in the comments how they turned out. I read every one.
Pumpkin Cheesecake Cookies Recipe
These pumpkin cheesecake cookies are soft pumpkin spice cookies made with butter, brown sugar, canned pumpkin puree, cinnamon, and pumpkin pie spice, filled with a sweet cream cheese center. The recipe makes 18 to 20 cookies in about an hour and a half, most of it chilling time. The cream cheese filling is chilled and piped into the wells after baking, so these cream cheese filled pumpkin cookies never leak or turn rubbery in the oven. Bake them for fall cookie trays, Thanksgiving dessert tables, Halloween parties, and bake sales. Bake the cookies a day ahead and fill them on the day you serve, then keep them in the fridge for up to 4 days.
Ingredients
- FOR THE PUMPKIN COOKIE BASE
- 1 cup (226g) unsalted butter, softened
- 1 cup (200g) light brown sugar
- 1/2 cup (100g) granulated sugar
- 3/4 cup (180g) canned pumpkin puree (not pumpkin pie filling)
- 1 large egg
- 2 teaspoons vanilla extract
- 2 1/2 cups (310g) all-purpose flour
- 1 teaspoon baking soda
- 1/2 teaspoon baking powder
- 1/2 teaspoon salt
- 1 tablespoon pumpkin pie spice
- 1 teaspoon ground cinnamon
- FOR THE CHEESECAKE FILLING
- 8 oz (226g) cream cheese, softened
- 1/4 cup (50g) granulated sugar
- 1 teaspoon vanilla extract
- 1 tablespoon all-purpose flour
Instructions
- MAKE THE CHEESECAKE FILLING:
In a medium bowl, beat the cream cheese until smooth and free of lumps. Add the granulated sugar, vanilla extract, and (optional) flour, and mix until completely smooth. If using flour, be sure to heat-treat it first by microwaving it in a bowl for 1 minute, stirring halfway through, or baking it at 300°F (150°C) for 5–7 minutes. Let it cool before using. Transfer the mixture to a piping bag or a zip-top bag with one corner snipped off. Chill in the refrigerator for at least 30 minutes while preparing the cookie dough. - MAKE THE PUMPKIN COOKIE DOUGH:
In a large bowl, beat together the butter, brown sugar, and granulated sugar until light and fluffy, about 2 to 3 minutes. Add the pumpkin puree, egg, and vanilla extract and mix until well combined. In a separate bowl, whisk together the flour, baking soda, baking powder, salt, pumpkin pie spice, and cinnamon. Gradually mix the dry ingredients into the wet ingredients until a soft dough forms. Cover and chill the dough for 30 minutes to help the cookies keep their shape while baking. - SHAPE AND BAKE THE COOKIES:
Preheat the oven to 350°F (175°C) and line two baking sheets with parchment paper. Scoop about 2 tablespoons of dough for each cookie and roll into balls. Place the dough balls 2 inches apart on the prepared baking sheets. Flatten each one slightly, then use your thumb or the back of a spoon to press a shallow well into the center of each dough ball. Bake for 12 to 14 minutes, or until the edges are set and the tops look just done. The centers may puff up during baking—this is normal. Remove from the oven and, while the cookies are still warm, gently press down the centers again to deepen the wells. Let the cookies cool on the baking sheets for 5 minutes, then transfer to a wire rack to cool completely. - FILL WITH CHEESECAKE:
Once the cookies are fully cooled, pipe about 1 to 1½ teaspoons of the chilled cheesecake filling into the center of each cookie. Smooth the top if desired. Chill the filled cookies in the refrigerator for 20 minutes to allow the filling to set before serving.
Notes
Use plain canned pumpkin puree, not pumpkin pie filling. Chill the dough so the cookies keep their wells. Press the centers again while the cookies are warm, but only fill them once they are completely cool. Heat-treat the optional flour before adding it to the filling. Store the filled cookies in an airtight container in the refrigerator for up to 4 days. Let them sit at room temperature for 5 to 10 minutes before serving for the softest texture. Unfilled cookies can be frozen; fill them after thawing.
Can you freeze these cookies?
Thank you.
Hi Lesley, yes you can freeze them, but there are two good ways to do it depending on when you want to enjoy them.
If you’d like to get ahead, you can bake the pumpkin cookies on their own and freeze them plain. Once thawed, add the cheesecake filling fresh. That keeps the texture of the filling smooth and avoids any risk of it turning a little grainy after freezing.
If you’d rather freeze them fully assembled, that works too. I’ve done it when I needed to prep for a busy holiday week. The key is to freeze them flat on a baking sheet first, then transfer to a container with parchment between layers. Thaw overnight in the refrigerator so the cheesecake center softens slowly and stays creamy.
I made these and they were delicious! I do have a question. They didn’t come out looking like your. Mine didn’t keep there thickness. The looked more pancakes with dome tops. I followed the instructions to the T. So im not sure where I went wrong. Because of this the icing is in a tight circle in the middle so you bite more cookie than icing. Also I tried different techniques for pressing down. Some I did slight pressure, some more and some I only made the thumb print. I have photos if that would help! But i will definitely make these again they were so good! Thank you so much for sharing this recipe!
I’m so glad you liked them, Linette. If they spread too much, the dough may have needed a bit more chilling or slightly more flour. Try refrigerating it for an extra 15–20 minutes next time, and they should hold their shape better.