Last Updated on September 15, 2023 by Sabrina Currie
These easy, cheesecake filled pumpkin thumbprint cookies take the flavors of fall to a whole new level with a decadent cream cheese filling. These yummy, chewy pumpkin cookies are full of simple ingredients, take less than 20 minutes to prep, only 10 minutes to bake and are less than 100 calories each!
Why This Recipe Is So Good!
One of things about fall is all of the warm scents that fill the air. These pumpkin cream cheese thumbprint cookies are filled with ingredients like pumpkin, cinnamon, nutmeg, and ginger. They are perfect for any fall gathering like Thanksgiving and make a gorgeous cookie for Christmas too!
There is nothing better than a soft, warm pumpkin cookie and when you fill it with a cheesecake filling, you get a perfect cookie recipe. Let's get cooking!
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I love the flavors of this season and use them often in recipes like Gingerbread Muffins, Cinnamon Rolls with Apple Pie Filling, and Apple Crumble Tartlets. If you love pumpkin recipes as much as I do, try this quick and easy Carrot Pumpkin Soup too! It's a great way to use up the leftover pumpkin puree.
Recipe Ingredients
With only 12 simple ingredients in the cookies, this easy recipe is a breeze. The filling is a basic cream cheese frosting that is super versatile and can be used in lots of different recipes! Watch the quick video below to see how truly easy these cookies are!
- Pumpkin- I used canned pumpkin puree which is quick, easy, and nutritious.
- Cream Cheese - This is the foundation in the cream cheese filling. You can use any brand, but I prefer Philadelphia brand for it's taste and texture.
- Powdered Sugar - For the smoothest frosting, powdered sugar, or icing sugar, is the best choice.
- Egg - Did you know that size large eggs are the standard in written recipes? Unless otherwise specified, use large eggs in every recipe, especially baked recipes, calling for eggs.
See recipe card for quantities.
Substitutions + Variations
- Pumpkin Pie Spiced - Replace the spices in this recipe for pumpkin pie spice to save time and to add even more yummy flavors. A small dusting of extra pumpkin pie spice on the top adds an extra fragrant scent to this great cookie recipe.
- Cinnamon Sugar Topped - Sprinkle a mixture of ½ tablespoon cinnamon powder and 2 tablespoons of granulated sugar over freshly iced cookies before the cream cheese mixture has set. This adds a festive sparkle and little extra cinnamon flavor to your pumpkin cheesecake cookies.
- Pumpkin Chocolate Chip Cookies - Top the icing with mini white, milk, semi-sweet or dark chocolate chips for a chocolatey variation.
- Nutty Pumpkin Cookies - Add crushed hazelnuts or pecans on top of the filling for a crunchy texture and fantastic flavor.
How To Video
Step-by-Step Instructions
I've broken up the steps into two parts. The first is for making the pumpkin cheesecake thumbprint cookies, and the second part is for that scrumptious cream cheese filling.
Tips Before Starting: Preheat oven to 350º and take your cream cheese, butter, and eggs out of the fridge so they can come to room temperature.
Pumpkin Cookies
Step 1. Preheat oven to 350º. Combine all-purpose flour, cinnamon, nutmeg, ginger, baking soda and salt to in a bowl.
Step 2. Whisk flour with other dry ingredients and set aside.
Step 3. In a separate large bowl, add sugar, brown sugar, and butter.
Step 4. Beat butter mixture until fluffy.
Step 5. Add egg and vanilla to the butter mixture and beat until well combined.
Step 6. Add pumpkin purée.
Step 7. Beat until pumpkin is fully incorporated.
Step 8. Add the flour mixture to the mixing bowl with the wet ingredients.
Step 9. Mix cookie dough until fully incorporated.
Step 10. Drop tablespoon-sized dollops onto parchment-lined baking sheets with a cookie scoop or tablespoon.
Bake 10 minutes until just done.
Remove from oven and press a deep indentation into the center of the cookies with the back end of a wooden spoon. Let cool on a wire cooling rack.
Step 11. Once cookies are completely cooled, fill each with the cream cheese icing using a piping bag.
Optional: Sprinkle with cinnamon sugar, pumpkin spice mixture, nuts or chocolate chips if desired.
Easy Cream Cheese Icing
Step 1. In a medium bowl, add cream cheese, butter, and vanilla extract. Beat with an electric mixer until fluffy. (Using a larger bowl than needed will help prevent your icing sugar from flying everywhere.)
Step 2. Add powdered sugar and beat until smooth. Use right away or cover with plastic wrap to prevent it from drying out.
Expert Tips
- Room temperature cream cheese, butter and eggs are easier to work with, so leave them out for a bit before starting your cookies.
- Use parchment paper (or silicone mats) for easy cleanup and perfect non-stick results every time. You can also grease your cookie sheet with shortening or block margarine instead.
- This cream cheese frosting is lovely on any dessert, so make extra for your cinnamon rolls, cakes, cupcakes, and other sweet treats.
Storage + Freezing
These chewy cookies will store well in a single layer in the refrigerator in an airtight container freezer bag. If you want to freeze them, do so before adding filling.
The cream cheese filling can be made ahead and frozen separately as well. Thaw at room temperature before piping into the pumpkin thumbprints.
The cookies and the frosting will keep in the freezer for up to 3 months.
Recipe FAQs
You can use either salted or unsalted butter. If you use salted, omit the ¼ teaspoon of salt in the cookie dough.
Pumpkin puree's only ingredient is pumpkin. It is cooked and has no additional ingredients. Pumpkin pie filling has spices and sugar added.
Yes! Store extra frosting in a plastic bag with as much air removed as possible and use it for future baking projects!
I hope you love these easy, cheesecake filled pumpkin thumbprint cookies as much as I do. Let me know in the comments if you try them! And if you like them, I'd love it if you could leave a star rating to review them.
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Related Recipes
If you have any questions or comments, you can find me on Instagram, Pinterest and Facebook. I try to answer any recipe related questions quickly as I know you might be in the middle of making it.
Also check out my FREE PRINTABLE meal planner to make menu planning and grocery shopping a breeze and my shopping guide. And if you like this recipe, I would love it if you give it a star rating in the recipe card.
Cheers and happy cooking, Friends! Sabrina
📖 Recipe
Easy Cheesecake Filled Pumpkin Thumbprint Cookies
Ingredients
For the cookies:
- 1 ¼ c all-purpose flour
- 1 teaspoon cinnamon
- ¼ teaspoon nutmeg
- ¼ teaspoon ginger
- ½ teaspoon baking soda
- ¼ teaspoon salt
- ½ butter softened
- ¼ c. packed brown sugar
- ¼ c white sugar
- 1 large egg
- ½ teaspoon vanilla extract
- ½ c pumpkin puree
For the filling:
- 2 tablespoon butter softened
- 4 tablespoon cream cheese 2 oz at room temperature
- 1 c powdered sugar
- ½ teaspoon vanilla extract
Instructions
- Preheat oven to 350º
- Combine dry ingredients in a small mixing bowl, and set aside.
- In a large mixing bowl, beat butter and sugars together until fluffy.
- Beat in egg, and then vanilla and pumpkin purée, beating until fully incorporated between each addition.
- Stir in flour mixture until fully mixed.
- Drop cookie dough by the tablespoon onto a parchment-lined baking sheet.
- Bake in center of oven for 10 minutes until just done. Firm but not brown.
- Remove from oven and immediately press a "thumbprint" into the center of each cooker using the back of a spoon (such as a ½ teaspoon measuring spoon or the end of a wooden spoon). Let cool completely before icing.
- While the cookies cool, combine cream cheese icing ingredients and beat together until smooth.
- Once cookies are completely cooled, fill each with icing using a piping bag with a star tip. *See notes below Sprinkle any add-on toppings on while the icing is still moist.
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