These holiday cookies are less sweet that a traditional thumbprint cookie, relying on a dark chocolate ganache filling instead of the more traditional sweet jellies or jam. They’re soft and slightly crumbly in texture, which I love in a good snacking or tea cookie. Turbinado sugar is chunkier than granulated sugar and won’t melt down in the same way — so it helps make the edges of these cookies look slightly sparkly – most appropriate for the season. If you have sanding sugar at home, that would work great to roll the cookies in as well (just don’t use it in the actual dough).
In a small heavy-bottomed pot over low heat (or in a microwave-safe bowl in the microwave), melt the dark chocolate, stirring often to avoid burning. Whisk until smooth and set aside.
In a small mixing bowl, whisk together both flours, cocoa powder and salt.
In the bowl of a stand mixer fitted with the paddle attachment, cream the butter and sugar on medium speed until pale and fluffy, about 3 minutes. Add the egg yolk and vanilla and beat a few times to combine. Scrape in the melted chocolate and beat until just incorporated. Slowly beat in the flour mixture until just combined. Cover bowl with plastic wrap and refrigerate until firm, about 30 minutes.
Preheat the oven to 350 F. Line a large baking sheet with parchment paper. Get a little bowl ready with extra turbinado sugar to roll the cookies in. Form balls using 1 tablespoon of dough for each, and roll in sugar. Place balls 1 inch apart on prepared baking sheet.
Use your thumb to press gently into the center of each cookie to create an indentation – be careful not to press all the way through the cookie and be sure the indentation is wide enough to hold the filling. The cookies may crack a little on the sides and that’s ok – that gives them character. If they crack significantly, I do a little quick push / pat back together.
Bake for 10 minutes, remove from oven and use your finger or the tip of a wooden spoon to reinforce the indentation if it’s started to puff back up in the baking process. Then place back in oven and bake until cookies are just set, about 8-9 minutes (they will still feel soft; they’ll firm up as they cool). Allow cookies to cool on baking sheets for 5 minutes. Transfer to wire racks to cool completely.
Meanwhile, make the chocolate ganache: In a heatproof bowl set over a pan of barely simmering water, melt the chocolate with the cream, stirring until smooth. Stir in the vanilla extract. Let cool until the mixture is thick and spoonable, like pudding, about 15 minutes. Gently spoon chocolate filling into the center of each cookie. Let stand until set, about 55 minutes. Sprinkle a pinch of flaky salt across the tops of each cookie. Cookies can be stored in an airtight container for up to 5 days.