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Cheesecake Thumbprint Cookies

Love cheesecake? You’ll love the cream cheese filling that makes these Cheesecake Thumbprint Cookies so very good!

stack of Cheesecake Thumbprint Cookies on a gray and white plate

Cream Cheese Thumbprint Cookies

If you find yourself looking for something a little different in the cookie world, look no further than these Cheesecake Thumbprint Cookies. Thumbprint cookies certainly aren’t anything new, but the addition of a cheesecake filling is definitely worth some excitement.

The cookies themselves are very simple in flavor and are made with just a few ingredients. Their simplicity combines magically with the richness of the cheesecake filling for a wonderfully delicious dessert.

three Cheesecake Thumbprint Cookies on a gray and white plate

There’s not a lot of obvious flavor happening in the cookie dough. In fact, you’ll find that these cookies aren’t overtly flavorful on their own. That lets the flavor of the cheesecake really shine. I do like to roll some of the cookies in cinnamon-sugar for a Snickerdoodle-like variation.

Both variations are really tasty. The original version is not overtly sweet, but the cookies are just lovely. To me, the simple cookie serves as almost the crust to the cheesecake. If you’re a big cheesecake fan, you’ll enjoy that the focus is decidedly on the cheesecake filling. Whereas the cinnamon-sugar twist adds a little kick of flavor.

Tips for Success

  • Measure accurately. Use a kitchen scale to measure by weight, or use the spoon and sweep method.
  • Use a cookie scoop. It will make quick work of portioning the dough and also ensure that your cookies are evenly sized.
  • Use homemade or store-bought cinnamon-sugar. If you want to make your own, use a 4:1 ratio of granulated sugar to ground cinnamon.
  • Re-form the indentations during and after baking if needed. Sometimes those indentions lose some of their shape. You can carefully use the end of a wooden spoon or some other tool to re-shape.
  • Chill the cookies after filling them. That will allow the filling to set.
  • Keep the cookies refrigerated. Bring them to room temperature before serving.
overhead view of Cheesecake Thumbprint Cookies on a marble surface

These Cheesecake Thumbprint Cookies are definitely a departure from standard cookie fare. And that’s a very good thing. Adding cream cheese is pretty much always a good idea in my book. And that beautiful, delicious filling really elevates these thumbprint cookies into something quite special!

Cheesecake Thumbprint Cookies

Yield about 30 cookies
Prep Time 30 minutes
Cook Time 28 minutes
Total Time 58 minutes

These simple thumbprint cookies get their flavor from the cheesecake filling!

stack of Cheesecake Thumbprint Cookies on a gray and white plate


For the filling:

  • 4 ounces (113g) cream cheese, softened
  • 1/4 cup (50g) granulated sugar
  • pinch salt
  • 1 large egg yolk
  • 1 & 1/2 teaspoons sour cream
  • 1/8 teaspoon vanilla extract

For the cookies:

  • 1 cup (226g) unsalted butter, softened
  • 1/4 cup (50g) granulated sugar
  • 1/4 teaspoon salt
  • 1 large egg yolk
  • 2 cups (240g) all-purpose flour
  • cinnamon sugar, optional*


To make the filling:

  1. Using an electric mixer on medium speed, beat the cream cheese until light and fluffy. Add the sugar and salt. Mix until smooth. Add the egg yolk, sour cream, and vanilla, and beat until smooth.
  2. Refrigerate for about 30 minutes.

To make the cookies:

  1. Preheat oven to 350°F. Line baking sheets with silicone liners or parchment paper.
  2. Using an electric mixer on medium speed, beat the butter and sugar until light and fluffy. Add the salt and egg yolk, and mix well.
  3. Reduce mixer speed to low. Gradually add the flour, mixing just until combined.
  4. Using 1 tablespoonful of dough at a time, roll the dough into balls. If desired, roll each ball in cinnamon-sugar. Place the cookies about an inch apart on the prepared pans.
  5. Make an indentation in the top of each ball with a small tart tamper or the handle of a wooden spoon. Flour the tamper or spoon if needed to prevent sticking.
  6. Bake 10 minutes. Remove from the oven and make indentations again. Bake 8-10 minutes, or until the edges begin to turn golden.
  7. Cool completely on the pans on wire racks.
  8. After the cookies have cooled, preheat oven to 350°F again.
  9. Fill the indentations with about 1 teaspoon of cream cheese filling. Mound the filling slightly.
  10. Bake the cookies 7-8 minutes, or until the filling is firm. Cool the cookies on the pans on wire racks for 5 minutes. Then, transfer the cookies to wire racks to cool completely.
  11. Transfer the cooled cookies to an airtight container. Place waxed paper or parchment paper between layers. Refrigerate at least 4 hours before serving.
  12. Allow the cookies to sit at room temperature for 15-20 minutes before serving.


*To make cinnamon sugar, mix 4 parts of granulated sugar with 1 part ground cinnamon.

Recipe adapted from Martha Stewart's Baking Handbook.

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    25 Comments on “Cheesecake Thumbprint Cookies”

  1. Love snickerdoodle too! Bite size cheesecake….ummmm, hello?!? Delish!

  2. These cookies look amazing – super yummy! Definitely need to try them. 🙂

  3. What a great filling for these cookies

  4. These would make a great addition to a holiday cookie exchange.

  5. Wonderful. Now, I am hungry.

  6. I used to buy these at my grocery store with a chocolate base that had mini chocolate chips in it. It was delicious and I was so sad when they stopped making them/I moved away. Any chance you might make these in a chocolate variety at some point?

  7. These look delish!

  8. Yum! Very excited for this series:)

  9. Looks like a great variation from the old jam standby!

  10. I am a big fan of cream cheese frosting so I imagine I’d LOVE these cookies! Such a fun twist on a classic.

  11. This is such a unique cookie, and I love all things cheesecake! Gotta try these!

  12. what wonderful cookie idea,i love all cheese cake recipes

  13. What a fun twist on a classic cookie. And I love snickerdoodles, so the cinnamon sugar coating sounds awesome!

  14. These look wonderful! =)
    Now…Im hungry.. lol

  15. These are genius! I love thumbprint cookies but the jam filling doesn’t do it for me- this sounds wonderful!

  16. Love these cookies! Pinned them for later.

  17. Wow! I have never heard of adding cheese to cookies, but this sounds delicious. I’m a huge cookie fan, but I’m getting bored of the classic chocolate chip or sugar cookie. This is such an innovative way of transforming cookies into a wonderfully inventive dish! I love how daring this is and I can’t wait to try it!

  18. These look so good! =)

  19. Do these cookies need to be refrigerated for storage, because of the egg & dairy, or can leftover cookies (assuming there are some) be left at room temp?

  20. A lovely variety for the holidays!

  21. Am I reading this wrong or are the cookies spending almost 1/2 hr in the oven? Is that correct?

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