Line a 9 x 13 inch pan with parchment and set aside.
In a medium bowl, whisk together the flour, cocoa powder and salt and set aside.
In the bowl of a stand mixer (or using hand beaters), beat the butter on medium speed, until light and fluffy, 4-5 minutes. Add the sugar in a few batches and continue to beat for another minute or so. Add vanilla extract, scrape down the edges of the bowl and beat again for 30 seconds or until well combined.
With the mixer on low, gradually add the dry ingredients and beat until just incorporated, about 1 minute. Fold in the cacao nibs.
Press the dough evenly into the prepared pan. Cover with plastic wrap and use the plastic wrap to help you to smooth out the top of your shortbread, using your hands or the back of a measuring cup. Refrigerate at least 2 hours and up to 1 day.
Preheat the oven to 350 F. Use a paring knife to slice dough into 27 bars (8 across the short side, 3 across the long side). Poke holes in the top using a fork.
Bake for 30 minutes. Let cool completely in pan. Once cool, recut bars along your original cut marks. Shortbread will remain fresh for up to 3 weeks if stored in an airtight room temperature container.