
Cheesecake Thumbprint Cookies
These cookies are like little bites of cheesecake. A tender butter-and-cream-cheese cookie is rolled in graham cracker crumbs, pressed with a deep center, and filled with a smooth cheesecake filling before baking. The graham coating gives the cookies a familiar cheesecake-crust flavor while the center stays creamy and tangy.
Ingredients
Equipment
Method
- Soften the butter and cream cheese. Both should be soft enough to blend easily but not melted or warm. If the butter looks shiny or oily, it has become too warm.
- Beat the butter, cream cheese, and sugar. Beat on medium speed for about 2-3 minutes, until smooth, creamy, and slightly fluffy. Scrape down the bowl.
- Add the egg and flavorings. Add the egg, vanilla, and lemon juice. Beat just until evenly combined.
- Mix the dry ingredients. In a separate bowl whisk together the flour, baking powder, and salt.
- Make the dough. Add the dry ingredients to the cream-cheese mixture. Mix on low speed only until the flour disappears and a soft dough forms. Do not overmix.
- Chill the dough. Cover and refrigerate for 1 hour. The dough should feel cool and firm enough to roll into balls without sticking heavily to your hands.
- Make the filling. Beat the softened cream cheese until completely smooth. Add the sugar, egg yolk, sour cream, lemon zest, vanilla, and pinch of salt. Beat until smooth and creamy, scraping the bowl as needed.
- Preheat the oven. Preheat to 350°F / 175°C. Line 2 baking sheets with parchment paper.
- Portion the dough. Divide the chilled dough into about 30 pieces, approximately 29 g each.
- Roll into balls. Roll each portion gently between your palms until round. If the dough becomes too soft while you work, refrigerate it for another 10-15 minutes.
- Coat in graham crumbs. Roll each dough ball completely in graham cracker crumbs. Place the balls about 2 inches / 5 cm apart on the prepared baking sheets.
- Make the cheesecake wells. Use the rounded back of a small measuring spoon to press a deep indentation into the center of each ball. Do not press all the way through the bottom.
- Fill the cookies. Spoon about 1 tsp / 6 g cheesecake filling into each indentation. Fill nearly to the top without mounding excessively.
- Bake. Bake at 350°F / 175°C for about 15-18 minutes. Start checking at 15 minutes. The edges should be lightly golden, the cookies should look set, and the cheesecake center should be just set but still creamy-looking.
- Cool on the pan. Leave the cookies on the baking sheet for 5 minutes because they are delicate when hot.
- Transfer and chill. Move carefully to a wire rack and cool completely. For the best cheesecake texture, refrigerate the cooled cookies for several hours before serving.
Notes
Storage
Store the cooled cookies in an airtight container in the refrigerator for up to 5 days. Place parchment paper between layers if stacking.
Freezing
Once completely chilled, freeze in a single layer until firm, then transfer to an airtight freezer-safe container with parchment between layers. Freeze for up to 2 months. Thaw overnight in the refrigerator.
Make Ahead
- Dough: Make and refrigerate for up to 24 hours before shaping.
- Filling: Prepare while the dough chills and keep refrigerated until ready to use.
- Finished cookies: These are excellent made the day before serving because chilling gives the cheesecake centers time to set.
- Raspberry Cheesecake: Add a tiny dot of raspberry preserves on top of the cheesecake filling.
- Strawberry Cheesecake: Add a small amount of thick strawberry preserves.
- Chocolate Cheesecake: Drizzle completely cooled cookies lightly with melted chocolate.


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