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Cheesecake Thumbprint Cookies

overhead view of Cheesecake Thumbprint Cookies on a white plate

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

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

There’s not a lot of obvious flavor happening in the cookie dough. I contemplated adding a bit more sugar or augmenting in some other way. Instead, I decided to roll some of them in cinnamon-sugar for a Snickerdoodle-like variation. Then, I could compare the two and decide which works better.

Cheesecake Thumbprint Cookies on a white plate

Honestly? I can’t pick. I love them both! 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.

With the cinnamon-sugar version, you get more flavor and sweetness in a quick and easy way. You can use a commercially available cinnamon-sugar, but it’s also very easy to make your own. The most common proportions are 1 tablespoon of cinnamon per 1/4 cup sugar. One of the perks of making your own is that you can adjust that to your taste.

These 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. 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
overhead view of Cheesecake Thumbprint Cookies on a 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 cream cheese until light and fluffy. Add sugar and salt. Mix until smooth. Add 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°. Line baking sheets with silicone liners or parchment paper.
  2. Using an electric mixer on medium speed, beat butter and sugar until light and fluffy. Add salt and egg yolk, and mix well.
  3. Reduce mixer speed to low. Gradually add flour, mixing just until combined.
  4. Using 1 tablespoonful of dough at a time, roll dough into balls. If desired, roll each ball in cinnamon-sugar. Place cookies about an inch apart on 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 oven and make indentations again. Bake 8-10 minutes, or until the edges begin to turn golden.
  7. Cool completely on pans on wire racks.
  8. After cookies have cooled, preheat oven to 350° again.
  9. Fill indentations with about 1 teaspoon of cream cheese filling. Mound the filling slightly.
  10. Bake cookies 7-8 minutes, or until filling is firm. Cool cookies on pans on wire racks for 5 minutes. Then, transfer cookies to wire racks to cool completely.
  11. Transfer cooled cookies to an airtight container. Place waxed paper or parchment paper between layers. Refrigerate at least 4 hours before serving.
  12. Allow 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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