I started making Pumpkin Cheesecake Thumbprints one chilly Sunday when the house smelled like wet leaves and my favorite sweater was still a little damp from the line. You know that muddle of a day. I baked a batch for a neighbor and accidentally kept half, because I tasted one and thought oh no these are staying. They are part cookie, part mini cheesecake, and entirely the kind of treat that makes you stand at the counter with a mug of coffee and say yep that hits. Also, I may or may not have snuck a second one while waiting for the kettle. Who is counting.
Why you might fall for these like I did
I make this when the weather turns bossy and all I want is something cozy but not fussy. My family goes a bit wild for the creamy center with the soft spiced cookie edges, and I love that the cheesecake bit sets up in the oven so I am not doing any water bath nonsense. If I am short on time, I use store cookie dough and it still works a charm, though honestly the homemade dough has better flavor. And if you have ever fought with sticky pumpkin puree and ended up with gloopy batter, same, but actually I find it works better if you pre bake the cookies a few minutes then fill them. Less spreading, less stress. Tiny win.
What you need, plus the swaps I have tried
- For the cookie dough
- 113 g unsalted butter, softened to room temp. I have browned it before for extra depth. If you want to try that, this guide is solid advice: Serious Eats brown butter tutorial.
- 100 g granulated sugar plus 50 g light brown sugar. If you only have one kind, use 150 g total and carry on.
- 1 large egg yolk. I save the white for a veggie omelette, or sometimes it just sits there and I forget it exists.
- 1 teaspoon vanilla extract. My grandmother always insisted on the fancy vanilla, but honestly any version works fine.
- 220 g all purpose flour which is about 1 and ¾ cups. If measuring by cups, fluff and spoon so you do not pack it. Or use a scale, it is easier. This guide is handy if you are a scooper: how to measure flour.
- 1 teaspoon pumpkin pie spice, or use ¾ teaspoon cinnamon plus small pinches of ginger, nutmeg, and clove. If you need a mix recipe, I like this one: simple spice blend.
- ½ teaspoon baking powder
- ½ teaspoon fine salt
- 1 to 2 tablespoons milk only if the dough seems dry and crumbly
- For the pumpkin cheesecake center
- 170 g cream cheese, softened. Full fat tastes best. The light stuff works, texture is just a bit less rich.
- 120 g pumpkin puree, not pumpkin pie filling. Canned is perfect. I sometimes use fresh puree if I have it knocking about.
- 50 g light brown sugar
- 1 teaspoon vanilla extract
- ¾ teaspoon pumpkin pie spice
- 1 tablespoon all purpose flour or 2 teaspoons cornstarch to help the filling set
- Pinch of salt
- Optional but lovely a little orange zest
- Optional toppings
- A handful of graham cracker crumbs for a faux crust vibe
- A shake of cinnamon sugar
- Caramel sauce and a pinch of flaky salt for serving
Let us make them together
- Heat the oven to 350 F which is 175 C. Line a baking sheet with parchment. I preheat first so I do not forget and end up waiting around later.
- Make the cheesecake center. In a bowl, beat the cream cheese until smooth, then mix in pumpkin puree, brown sugar, vanilla, spice, flour, and salt. It should be creamy and a bit thick. Pop it in the fridge while you do the dough.
- For the dough, beat the softened butter with the sugars until the color lightens and it looks fluffy. About 2 to 3 minutes with a hand mixer. Add the egg yolk and vanilla and mix just until combined.
- Whisk the flour, pumpkin spice, baking powder, and salt together. Add to the butter mixture in two parts, mixing on low until no dry streaks remain. If it feels sandy and will not come together, drizzle in milk a teaspoon at a time. This is where I usually sneak a tiny taste.
- Scoop dough into small balls, roughly 1 tablespoon each. A cookie scoop makes this tidy. If you do not have one, two spoons and a patient mood will do. Roll the balls between your palms to smooth them and set on the tray with a bit of space between.
- Chill the tray in the freezer for about 10 minutes. Not required, but it helps keep the cookie shape. Sometimes I skip it and they still behave, so do what suits.
- Bake for 6 minutes, then pull the tray and use the back of a measuring teaspoon or your thumb to press a well into each cookie. Do not be shy, make a good little pool for the filling. If the edges crack a smidge, press them back together.
- Spoon or pipe a heaping teaspoon of the pumpkin cheesecake filling into each well. I like to mound it slightly. Sprinkle graham crumbs if using.
- Return to the oven and bake 6 to 8 more minutes until the cookies look set at the edges and the filling barely jiggles. Do not wait for browning on the filling, it will firm as it cools.
- Cool on the tray for 10 minutes, then move to a rack. I think these taste even better after a short chill in the fridge, about 30 minutes. Do we really need to wait. Probably. But I always eat one warm anyway, because I am only human.
Notes form my kitchen
- Too much pumpkin can make the filling watery. We are keeping it at about 120 g, which sets up nicely with that little bit of flour.
- If your dough is cracking a lot when you press the wells, it might be a touch dry. Next time add a teaspoon of milk, or do not chill quite as long.
- Spice levels are personal. If yours is fresh and bold, you may want less. If your spice jar is older than your phone, add a pinch more.
- Weighing flour gives the most consistent texture. Cups are fine, but it is easy to pack them. I say this with love as a reformed scooper.
Variations I have played with
- Brown butter cookie dough. Nutty, deeper flavor, slightly crisper edges. Great with a pinch of flaky salt on top.
- Chocolate swirl. Add a little spoon of melted dark chocolate on the filling and swirl with a toothpick. Looks fancy, zero stress.
- Maple version. Swap half the brown sugar in the filling for real maple syrup, then add 1 more teaspoon of flour to keep it set.
- One that did not work. I tried adding chopped pecans into the dough and went a bit heavy. The cookies crumbled and the centers leaked. Next time I will just press a few on top.
Gear I use, plus a workaround if you are short on tools
- A hand mixer or stand mixer for smooth filling and fluffy butter sugar. A whisk works if you are feeling strong, but it takes longer.
- A small cookie scoop. I call it essential for tidy cookies, then I remember two spoons also do the job. So it is essential, except when it is not.
- Parchment lined baking sheet. No parchment. Lightly butter the sheet and keep an eye on them.
- Measuring teaspoon for the wells, or your thumb, which nature kindly provided.
How to store these little beauties
Because of the cheesecake center, keep leftovers in an airtight container in the fridge for up to 4 days. They freeze well for about 2 months. Freeze flat on a tray, then pop into a bag. Thaw in the fridge so the texture stays nice. Though honestly, in my house it never lasts more than a day.
Serving ideas that make me happy
- Dust with powdered sugar right before serving for a pretty finish.
- Add a dot of whipped cream and a tiny sprinkle of spice for holiday vibes.
- Coffee or hot cider on the side is the move. Late night nibble with a cold glass of milk also hits different.
- Family tradition alert. We pass a small bowl of graham crumbs at the table so people can dunk the tops. Silly, fun, works every time.
Pro tips I learned the hard way
- I once tried rushing the chill and pressed the wells too soon. The cookies collapsed and looked grumpy. A short bake first, then press, makes all the difference.
- I piled the filling too high once, because greed. It overflowed and glued a few to the pan. Leave a little space at the edges.
- I forgot the salt in the dough, and the whole batch tasted flat. Just a pinch wakes up the pumpkin and spice.
- Its tempting to use the whole egg in the dough. The extra white can make them cakey and puffy. The yolk alone keeps them tender and neat.
FAQ friends keep asking me
Can I use canned pumpkin pie mix
Yes, but it is already sweetened and spiced, so cut the brown sugar in the filling to about 25 g and skip the extra spice. The flavor will be a bit different, still lovely.
Do these need to be refrigerated
Yep. Cheesecake center means fridge. Serve cold or let them sit out 15 minutes. They get extra creamy when the chill comes off.
Help, my cookies spread too much
Chill the scooped dough briefly, bake the first few minutes before adding the filling, and make sure the butter was just softened not melty. Also check your oven temp. An inexpensive oven thermometer changed my bakes, no kidding.
Gluten free, possible
Use a one to one gluten free flour blend that includes xanthan gum. I reckon the texture is slightly more delicate, but still very good. Keep an eye on bake time, they might need an extra minute.
Can I make them ahead
Yes. Bake, cool, and refrigerate up to 2 days. Or freeze baked cookies, then thaw in the fridge. You can also freeze the unbaked dough balls and the filling separately, then bake from chilled and fill as directed.
Could I use store dough
Short answer, sure. Sugar cookie dough works. I like to add a pinch of pumpkin spice to the dough and a smidge of salt to keep it from tasting too sweet.
Random but true, I once traded a dozen of these for the biggest butternut squash you have ever seen, from a neighbor who calls everyone love. Worth it. Anyway, enjoy baking, and if you try these Pumpkin Cheesecake Thumbprints, tell me how it went. Or if they vanished before you could blink, tell me that too.
Ingredients
- 8 oz (225 g) cream cheese, softened, divided (6 oz for dough, 2 oz for filling)
- ½ cup (115 g) unsalted butter, softened
- ¾ cup (150 g) granulated sugar
- 1 large egg (for dough)
- 1 teaspoon vanilla extract
- 2 cups (250 g) all-purpose flour
- ½ teaspoon baking powder
- ¼ teaspoon salt
- ½ cup pumpkin puree (for filling)
- 2 tablespoons packed brown sugar (for filling)
- 1 teaspoon pumpkin pie spice (or ½ teaspoon cinnamon + ¼ teaspoon ginger + ¼ teaspoon nutmeg)
- Optional: powdered sugar for dusting
Instructions
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1Make the dough: In a large bowl, beat 6 oz softened cream cheese and the butter until smooth. Add granulated sugar and egg, mixing until light and creamy. Stir in vanilla.
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2Combine dry ingredients: Whisk together the flour, baking powder, and salt in a separate bowl. Gradually add the dry mix to the wet ingredients and mix until a soft dough forms. If dough is sticky, chill 15 minutes.
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3Shape and bake: Preheat oven to 350°F (175°C). Roll dough into 1-inch balls and place 1 inch apart on a parchment-lined baking sheet. Use your thumb or the back of a small spoon to press an indentation into the center of each ball. Bake for 10–12 minutes, until edges are set and bottoms are lightly golden. Cool on the baking sheet 5 minutes, then transfer to a wire rack.
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4Prepare pumpkin cheesecake filling: In a small bowl, beat the remaining 2 oz cream cheese until smooth. Stir in pumpkin puree, brown sugar, and pumpkin pie spice until well combined and creamy.
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5Fill the cookies: Once cookies are mostly cooled, spoon or pipe about ½ teaspoon of the pumpkin cheesecake filling into each thumbprint indentation. Return to the refrigerator to chill and set for at least 1 hour.
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6Serve: Optionally dust with powdered sugar before serving. Store leftover cookies in an airtight container in the refrigerator for up to 4 days.
Approximate Information for One Serving
Nutrition Disclaimers
Number of total servings shown is approximate. Actual number of servings will depend on your preferred portion sizes.
Nutritional values shown are general guidelines and reflect information for 1 serving using the ingredients listed, not including any optional ingredients. Actual macros may vary slightly depending on specific brands and types of ingredients used.
To determine the weight of one serving, prepare the recipe as instructed. Weigh the finished recipe, then divide the weight of the finished recipe (not including the weight of the container the food is in) by the desired number of servings. Result will be the weight of one serving.
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