In a large mixing bowl, whisk together the flour, salt, cinnamon, and nutmeg, and set it aside.

In the bowl of a stand mixer fitted with the paddle attachment or in a large mixing bowl with an electric handheld mixer, cream the butter and sugars together for 5 to 7 minutes until light and fluffy. Start on low speed (3-4) and gradually increase the speed to high (8-9).

Add the vanilla and mix on medium until combined. Add the flour mixture to the bowl and beat until just a few spots of dry flour remain. Start on low speed and gradually increase to medium-high. Do not overmix the dough.

Add the pecans to the bowl and mix on low until they are evenly distributed into the dough. Cover the bowl with plastic wrap and refrigerate for at least 30 minutes up to overnight.

Preheat your oven to 325°F. Line a baking sheet with parchment paper or a silicone baking mat. Using a medium cookie scoop, scoop out about 1 ½ tablespoons of dough and roll them into balls with both palms.

Place the dough balls on the lined baking sheet about 2 inches apart. Wet the flat bottom of a glass and press down on the cookie balls slightly to flatten them into ½-inch thick cookies. Gently press a pecan half into the top of each cookie.

Bake the cookies on a middle rack in the preheated oven for 17 to 20 minutes or until the edges just start to turn light golden brown. Allow the cookies to cool on the baking sheet for 5 minutes then transfer them to a wire rack to cool completely.