Tasty Pumpkin Cream Cheese Thumbprint Cookies

Here is my favorite pumpkin cream cheese thumbprint cookie recipe, with soft pumpkin spice cookies, a creamy tangy cream cheese filling, and just the right amount of fall flavors.

These thumbprint cookies are what I reach for every October when I want something cozy but not too heavy. My kids love helping me make the little wells in each cookie, and honestly, they disappear from the cookie jar faster than I can make them.

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What Kind of Pumpkin Puree Should I Use?

For these thumbprint cookies, you’ll want to use plain canned pumpkin puree, not pumpkin pie filling which already has spices mixed in. Look for brands like Libby’s or store brands that list only pumpkin as the ingredient – avoid anything labeled “pumpkin pie mix” since we’re adding our own spice blend. If you have fresh pumpkin on hand, you can certainly roast and puree your own, but canned pumpkin is convenient and gives consistent results every time. Just make sure to give the can a good stir before measuring, as the puree can sometimes separate slightly.

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Options for Substitutions

These cookies are pretty forgiving when it comes to swaps, so here are some options if you need to make changes:

• Canned pumpkin puree: You can substitute with sweet potato puree or butternut squash puree for a similar texture and flavor. Just make sure it’s plain puree without any added spices.
• Individual spices: Don’t have all the spices on hand? You can replace the cinnamon, ginger, nutmeg, and cloves with 2 teaspoons of pumpkin pie spice instead.
• Light brown sugar: If you only have dark brown sugar, that works too – it’ll just give the cookies a slightly deeper molasses flavor. You can also use all white sugar if needed.
• All-purpose flour: For a slightly nuttier flavor, you can replace up to half the all-purpose flour with whole wheat flour, but don’t go beyond that or the cookies might get too dense.
• Cream cheese: The cream cheese is really what makes these thumbprints special, so I wouldn’t recommend substituting it. Make sure it’s block-style and fully softened for the smoothest filling.
• Unsalted butter: You can use salted butter if that’s what you have – just reduce the salt in the recipe to 1/4 teaspoon to balance things out.

Watch Out for These Mistakes While Baking

The biggest mistake with pumpkin thumbprint cookies is using cream cheese and butter that aren’t properly softened, which leads to lumpy filling that won’t pipe smoothly – let both ingredients sit at room temperature for at least an hour before mixing.

Another common error is making the thumbprint indentations too shallow or waiting until the cookies are fully baked, so press your thumb (or a small spoon) into the dough balls before baking and make the wells deep enough that they won’t disappear as the cookies spread.

Don’t skip chilling the dough for 30 minutes if it feels too sticky to handle, and be sure to use canned pumpkin puree rather than pumpkin pie filling, which contains added spices that can throw off the flavor balance.

Finally, let the cookies cool completely before adding the cream cheese filling, otherwise the warmth will cause it to melt and run off the cookies.

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What to Serve With Pumpkin Cream Cheese Thumbprint Cookies?

These soft, spiced cookies are perfect with a warm cup of coffee or chai tea – the cream cheese filling pairs so nicely with those cozy fall flavors. I love serving them alongside a steaming mug of hot chocolate or even a glass of cold milk for dunking. They’re also great as part of a dessert spread with other fall treats like apple cider donuts or caramel apples. For something a little different, try them with a scoop of vanilla ice cream or even a drizzle of caramel sauce on top of that creamy filling.

Storage Instructions

Keep Fresh: These pumpkin thumbprint cookies stay soft and delicious when stored in an airtight container at room temperature for up to 5 days. Just make sure the cream cheese filling has set completely before stacking them, or use parchment paper between layers to keep them from sticking together.

Refrigerate: Since these cookies have cream cheese filling, I like to keep them in the fridge if I’m storing them for more than a couple days. They’ll stay fresh in the refrigerator for up to a week and actually taste really good chilled – almost like little cheesecake bites!

Freeze: You can freeze these cookies for up to 3 months in a freezer-safe container with parchment between the layers. Let them thaw at room temperature for about 30 minutes before serving. The texture holds up really well, making them perfect for holiday baking ahead of time.

Estimated Nutrition

Estimated nutrition for the whole recipe (without optional ingredients):

• Calories: 3200-3500
• Protein: 28-34 g
• Fat: 165-185 g
• Carbohydrates: 420-470 g

Ingredients

For the cookies:

• 10 tbsp unsalted butter, at room temperature
• 3/4 cup granulated sugar
• 1/2 cup packed light brown sugar
• 1 cup plain canned pumpkin puree
• 1 large egg
• 2 cups all-purpose flour
• 1 tsp baking soda
• 1/2 tsp baking powder
• 3/4 tsp salt
• 1 1/2 tsp ground cinnamon
• 1/2 tsp ground ginger
• 1/2 tsp ground nutmeg
• 1/8 tsp ground cloves
• 1 tsp vanilla extract

For the cream cheese filling:

• 5 tbsp unsalted butter, softened
• 4 oz cream cheese (block style), softened
• 2 cups confectioners’ sugar
• 1/2 tsp vanilla

For garnish:

• Ground cinnamon for sprinkling

Step 1: Prep Baking Sheets and Preheat Oven

Preheat your oven to 350°F (175°C).

Line two baking sheets with silicone mats if you have them, or use parchment paper for easy cleanup and to prevent sticking.

Step 2: Prepare Wet Ingredients

• 10 tbsp unsalted butter, at room temperature
• 3/4 cup granulated sugar
• 1/2 cup packed light brown sugar
• 1 cup plain canned pumpkin puree
• 1 large egg
• 1 tsp vanilla extract

In a large mixing bowl, add 10 tablespoons of room temperature unsalted butter and beat until light and fluffy.

Gradually add in the 3/4 cup granulated sugar and 1/2 cup packed light brown sugar, mixing until smooth.

Next, incorporate 1 large egg, 1 cup plain canned pumpkin puree, and 1 teaspoon vanilla extract.

Mix all wet ingredients using an electric mixer until well combined.

Step 3: Combine Dry Ingredients and Make Dough

• 2 cups all-purpose flour
• 1 tsp baking soda
• 1/2 tsp baking powder
• 3/4 tsp salt
• 1 1/2 tsp ground cinnamon
• 1/2 tsp ground ginger
• 1/2 tsp ground nutmeg
• 1/8 tsp ground cloves

In a medium bowl, whisk together 2 cups all-purpose flour, 1 teaspoon baking soda, 1/2 teaspoon baking powder, 3/4 teaspoon salt, 1 1/2 teaspoons ground cinnamon, 1/2 teaspoon ground ginger, 1/2 teaspoon ground nutmeg, and 1/8 teaspoon ground cloves.

Slowly add these dry ingredients to the wet mixture, mixing until just combined.

Don’t overmix—stop as soon as the flour disappears into the batter.

Step 4: Portion, Bake, and Shape Cookies

• dough from Step 3

Using a spoon or a 1 1/2 tablespoon cookie scoop (slightly heaping), scoop the dough onto the prepared baking sheets, spacing each about 2 inches apart.

Bake one sheet at a time for 13-15 minutes, until the cookies are just browned at the edges.

Once removed from the oven, carefully make an indent in the center of each warm cookie with your finger.

Leave the cookies on the baking sheet briefly, then transfer to a wire rack to cool completely.

I like to make the indent while the cookies are still warm because the dough is softer and less likely to crack.

Step 5: Prepare Cheesecake Filling

• 5 tbsp unsalted butter, softened
• 4 oz cream cheese (block style), softened
• 2 cups confectioners’ sugar
• 1/2 tsp vanilla

While the cookies are cooling, make the cheesecake filling.

In a medium bowl, blend 5 tablespoons unsalted butter (softened), 4 ounces softened block-style cream cheese, and 1/2 teaspoon vanilla with an electric mixer until very light and fluffy.

Gradually add 2 cups confectioners’ sugar, mixing until the frosting is smooth.

Leave the filling at room temperature for easy spreading.

I find the filling is much easier to handle if you don’t refrigerate it right away.

Step 6: Assemble and Finish the Cookies

• baked cookies with indents from Step 4
• cheesecake filling from Step 5
• ground cinnamon for sprinkling
• 1/2 cup packed light brown sugar (for sprinkling)

Once the cookies have cooled for about 15 minutes, fill each center indent with a generous spoonful of the cheesecake filling from Step 5.

Sprinkle a little brown sugar and a pinch of ground cinnamon over the top for added flavor and a beautiful finish.

Store the cookies in an airtight container with wax paper between the layers, and keep refrigerated.

Bring to room temperature before serving for the best texture and taste.

To boost the flavor even more, I like to add a little extra cinnamon on top just before serving.

Tasty Pumpkin Cream Cheese Thumbprint Cookies

Delicious Tasty Pumpkin Cream Cheese Thumbprint Cookies recipe with step-by-step instructions.

Print Recipe Pin Recipe

Prep Time 25 minutes mins

Cook Time 50 minutes mins

Total Time 1 hour hr 15 minutes mins

Servings 4

Calories 3350 kcal

Ingredients

  

For the cookies:

• 10 tbsp unsalted butter, at room temperature
• 3/4 cup granulated sugar
• 1/2 cup packed light brown sugar
• 1 cup plain canned pumpkin puree
• 1 large egg
• 2 cups all-purpose flour
• 1 tsp baking soda
• 1/2 tsp baking powder
• 3/4 tsp salt
• 1 1/2 tsp ground cinnamon
• 1/2 tsp ground ginger
• 1/2 tsp ground nutmeg
• 1/8 tsp ground cloves
• 1 tsp vanilla extract

For the cream cheese filling:

• 5 tbsp unsalted butter, softened
• 4 oz cream cheese (block style), softened
• 2 cups confectioners' sugar
• 1/2 tsp vanilla

For garnish:

• ground cinnamon for sprinkling

Instructions

 

• Preheat your oven to 350°F (175°C). Line two baking sheets with silicone mats if you have them, or use parchment paper for easy cleanup and to prevent sticking.
• In a large mixing bowl, add 10 tablespoons of room temperature unsalted butter and beat until light and fluffy. Gradually add in the 3/4 cup granulated sugar and 1/2 cup packed light brown sugar, mixing until smooth. Next, incorporate 1 large egg, 1 cup plain canned pumpkin puree, and 1 teaspoon vanilla extract. Mix all wet ingredients using an electric mixer until well combined.
• In a medium bowl, whisk together 2 cups all-purpose flour, 1 teaspoon baking soda, 1/2 teaspoon baking powder, 3/4 teaspoon salt, 1 1/2 teaspoons ground cinnamon, 1/2 teaspoon ground ginger, 1/2 teaspoon ground nutmeg, and 1/8 teaspoon ground cloves. Slowly add these dry ingredients to the wet mixture, mixing until just combined. Don’t overmix—stop as soon as the flour disappears into the batter.
• Using a spoon or a 1 1/2 tablespoon cookie scoop (slightly heaping), scoop the dough onto the prepared baking sheets, spacing each about 2 inches apart. Bake one sheet at a time for 13-15 minutes, until the cookies are just browned at the edges. Once removed from the oven, carefully make an indent in the center of each warm cookie with your finger. Leave the cookies on the baking sheet briefly, then transfer to a wire rack to cool completely. I like to make the indent while the cookies are still warm because the dough is softer and less likely to crack.
• While the cookies are cooling, make the cheesecake filling. In a medium bowl, blend 5 tablespoons unsalted butter (softened), 4 ounces softened block-style cream cheese, and 1/2 teaspoon vanilla with an electric mixer until very light and fluffy. Gradually add 2 cups confectioners' sugar, mixing until the frosting is smooth. Leave the filling at room temperature for easy spreading. I find the filling is much easier to handle if you don't refrigerate it right away.
• Once the cookies have cooled for about 15 minutes, fill each center indent with a generous spoonful of the cheesecake filling from Step 5. Sprinkle a little brown sugar and a pinch of ground cinnamon over the top for added flavor and a beautiful finish. Store the cookies in an airtight container with wax paper between the layers, and keep refrigerated. Bring to room temperature before serving for the best texture and taste. To boost the flavor even more, I like to add a little extra cinnamon on top just before serving.