Position the racks in the lower and upper thirds of the oven and preheat the oven to 325°F. Line two baking sheets with Silpats or parchment paper.

Combine the flour and cocoa powder in a small bowl. Combine the nibs and sea salt in another small bowl.

In the bowl of a stand mixer fitted with the paddle attachment, cream the butter and sugar on medium speed for about 5 minutes, or until light and fluffy, stopping as necessary to scrape the sides and bottom of the bowl. Mix in the vanilla. Add about half of the flour mixture and mix on low speed. Add the remaining flour-cocoa mixture, stopping as necessary to scrape the bowl. Once incorporated, mix on medium speed for 1 to 2 minutes. Mix in the nibs and salt. (The dough can be refrigerated, well wrapped, for up to 1 week or frozen for up to 2 months.)

On a lightly floured board, or between two pieces of parchment paper, roll the dough into a square ¼ inch thick. Cut into 1 by 2½-inch rectangles or other desired shape, by hand or with a cookie cutter, and place on the prepared pans about 1 inch apart.

Bake for 15 minutes, rotating the pans once halfway through baking. It is sometimes difficult to know when chocolate cookies are done. One of the best indications is the scent of baked cookies in the air. And when these shortbread cookies are gently nudged, they shouldn’t feel soft but the bottoms should seem crisp.

Remove the pans from the oven and transfer the shortbread to a cooling rack to cool completely.

The cookies can be stored in an airtight container for up to 1 week.