Chocolate Thumbprint Cookies

These chocolate thumbprint cookies are like a traditional thumbprint cookie except they’re filled with chocolate instead of jam. Because who doesn’t want a chocolate-filled chocolate cookie?

Nine chocolate thumbprint cookies and a chocolate covered spoon on a round wooden board.

These are not your traditional thumbprint cookies. These subtly sweet, crumbly, European-style cookies are reminiscent of biscotti. As such, they’re perhaps best reserved for an adult palate rather than your second grader’s class party.–Renee Schettler

Chocolate Thumbprint Cookie

  • Quick Glance
  • (1)
  • 45 M
  • 1 H, 25 M
  • Makes 48 to 72 cookies
5/5 - 1 reviews
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  • For the cookies
  • For the filling


Make the cookies

Preheat the oven to 350°F (176°C). Position the oven racks in the top third and center of the oven. Line 2 large rimmed baking sheets with parchment paper or silicone baking mats.

Melt the chocolate in a small bowl set over (but not touching) a pan of simmering water or in a microwave-safe medium bowl on medium (50% power), stirring every 30 seconds. Stir until melted and smooth. Remove from the heat and let stand, stirring occasionally, until tepid but still fluid.

In a medium bowl, whisk together the flour and salt. In a large bowl, beat the butter, granulated sugar, and brown sugar with an electric mixer set on high speed until combined, about 1 minute. 

Beat in the egg yolks, 1 at a time, followed by the melted chocolate and the vanilla. With the mixer on low speed, mix in the flour mixture just until combined. (You can cover and refrigerate the dough for up to 24 hours. Return to room temperature before continuing.)

Using a heaping teaspoonful (or more) for each cookie, roll the dough into marble-sized balls and place them on a platter. (Your yield will vary depending on the size of the cookies.)

Tester tip: Forget your marble sizes? We did a little trial and error and found that we vastly prefer shooter-size blobs of dough as opposed to peewees, seeing as the bigger the blob, the softer and chewier the cookie.

Beat the egg whites in a small bowl until foamy. Place the pecans on a plate. One at a time, dip each dough ball in the whites, allowing any excess to drip off. Then roll the dough in the pecans and space the dough balls 1 1/2 inches apart on the prepared baking sheets. 

Using the end of a wooden spoon, press an indentation into the center of each cookie. (If the tip of the spoon handle sticks to the cookie dough, simply dust it with a little cocoa.) Refrigerate any dough balls that don’t fit on the plate until ready to bake.

Bake the cookies, rotating the positions of the sheets from top to bottom and front to back halfway through baking, until the edges appear set, about 10 minutes. 

Remove the baking sheets from the oven, and, using the end of the wooden spoon, reform the center indentation in each cookie. Return to the oven and continue baking until the edges of the cookies are crisp, 5 to 10 minutes more, depending on their size. 

Let the cookies cool on the baking sheets for 5 minutes. Transfer to wire cooling racks and let cool completely. Repeat with the remaining dough balls.

Make the filling

Melt the chocolate and oil in a small bowl set over (but not touching) a pan of simmering water or in a microwave-safe medium bowl on medium (50% power), stirring at 30-second intervals. Stir until melted and smooth.

Using a teaspoon, fill the indentations on each cookie with some of the chocolate mixture. Let stand until the chocolate sets (or, if you’re the impatient sort, you can refrigerate them to speed things up). Originally published December 14, 2012.

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Recipe Testers' Reviews

I love these cookies because they’re not overly sweet. I had refrigerated the dough and the hardest part was that when making the thumbprint, the chilled cookie dough would crumble a tad, so I had to try to fix them a little.

I made two versions, one with normal flour and the other with gluten-free flour. I noticed I had to add about 1 tablespoon more GF flour to get the same consistency as the first batch. I also made half a batch with the pecans and half without, and both were great even though the pecans do give a nice texture and taste.

I have a houseguest who is Italian and she didn’t rate these cookies a 10 only because she has a family biscotti recipe that she puts above it. We really liked these.

I cheated a little and rolled only half the dough in the egg whites and the pecans; the other half I just rolled, made indents, and baked. The ones rolled in the pecans are very good, just a tad drier (I really don’t mean that in a negative way). For the ones that I didn’t roll, I sprinkled the remaining chopped pecans on top of the melted chocolate. I used a small cork from an olive oil bottle to make my indentations. The dough stuck a bit to the cork so I dipped it in cocoa powder to help it release.

I’ll make these again—in fact I was thinking I might do these when I have the gals over for cookie baking day. Thinking I might put some espresso or mint in the chocolate filling. My houseguest and I are thinking of all kinds of variations on this cookie.


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  1. It is really hard to resist the sweetness of chocolates. This recipe is divine and I really like the chocolate at the center. It looks great and not just your typical chocolate chip cookie.

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