For the cookies:
1 cup (145g) rye flour
3/4 cup (90g) spelt flour
1/3 cup (30g) unsweetened Dutch-process cocoa powder
1 teaspoon kosher salt
4 ounces bittersweet chocolate (at least 60% cocoa), chopped
2 ounces semisweet chocolate chips
1 cup (2 sticks) unsalted butter, room temperature
1/2 cup (120g) natural cane sugar (like turbinado), plus more for rolling
1 large egg, room temperature
1 teaspoon pure vanilla extract
For the filling:
4 ounces semisweet chocolate chips
3 tablespoons unsalted butter
1/2 teaspoon pure peppermint extract
Crushed candy canes, for garnish
In a medium mixing bowl, whisk the rye and spelt flour with the cocoa powder and salt. Set aside. In a microwave-safe bowl, melt the bittersweet and semi-sweet chocolates on low until just melted. Whisk well until smooth, then set aside to cool slightly.
In the bowl of a stand mixer fitted with the paddle attachment (or using an electric mixer), beat the butter until light and creamy, about 2 minutes. Add the sugar and beat on medium until fluffy, another 2 minutes. Add the egg and vanilla and beat until just combined. Pour the melted and slightly cooled chocolate into the mixer and beat just until incorporated.
Add the flour and cocoa into the mixer bowl in two rounds, beating at low speed in between each addition. Scrape the sides of the bowl as needed. Chill the dough in the refrigerator until firm enough to roll into balls, about 30 minutes. Meanwhile, preheat the oven to 350°F.
Line 2 baking sheets with silicone baking mats or parchment paper. Spoon the coarse sugar into a small, shallow bowl. Scoop up roughly 2 tablespoons of the chilled dough and form into balls. Roll in the coarse sugar and transfer to the baking sheets. Using your thumb or index finger, press down firmly into the center of each cookie to form an indentation. Bake the cookies for 12 to 14 minutes, or until dry on top and slightly firm. Once out of the oven, press down gently on the indentations again to reinforce them, and transfer the cookie sheets to racks to cool completely.
Meanwhile, make the filling: In a microwave-safe bowl, microwave the semi-sweet chocolate chips and butter until melted. Stir in the peppermint extract. Set aside until slightly thickened, about 5 minutes. Using a teaspoon and working neatly, spoon the chocolate filling into the indents in the cookie. Gently sprinkle crushed candy cane bits onto the center of the cookie if you like – or leave as is. Allow the filling to set at room temperature before serving, about 20 to 30 minutes. Cover leftover cookies in an airtight container for 2 to 3 days.