Preheat oven to 325°F // 160°C // Gas mark 3.
In the bowl of a food processor fitted with a blade, pulse together flour, sugar, lemon thyme, kosher salt and lemon zest.
Add cubes of cold butter and pulse until crumbs form. The mixture should look sandy, it should not be smooth.
Add mixture to an ungreased 8x8 pan, and press dough down to flatten. (I like to use a flexible plastic bench scraper to clean up the edges and press the top of the dough flat).
Using a fork, skewer or toothpick, dock the dough (make holes in it) to let the steam escape.
Sprinkle the top with 1 teaspoon each of coarse sugar and flaky sea salt, if desired.
Bake for 45 - 50 minutes, rotating pan halfway through, to ensure even baking.
Remove from oven and let cool for 5 - 10 minutes. Remove from pan and gently cut shortbread while it is still warm.
Place cookies on wire rack to cool completely. Garnish with thyme leaves, if desired.