Place pecans in a large, light-colored skillet over medium heat. Cook, stirring constantly until pecans are toasted, about 5 minutes. Pour pecans into a small bowl and set aside to cool.

Wipe out the skillet with a paper towel. Add butter to the skillet, and place it back over medium-low heat. Cook, stirring frequently, until butter begins to brown and smell nutty, 5 to 7 minutes. Pour browned butter into a large mixing bowl and allow to cool for 20 minutes.

Preheat the oven to 350 degrees F. Line two baking sheets with silicone baking mats or parchment paper.

Add brown sugar and white sugar to the mixing bowl with cooled browned butter; and mix until combined. Add in egg, egg yolk, and vanilla and mix until thoroughly incorporated. Add in 1 1/4 cups flour, baking powder, salt, baking soda, and nutmeg and mix until just combined. Add in remaining 1 1/4 cups flour and mix until just combined. Stir in toasted pecans. Dough will be somewhat thick.

Scoop out 3 tablespoons of dough and roll into a ball. Repeat with remaining dough. Place dough balls about 1 1/2 inches apart on prepared baking sheets, and flatten balls to about 1/2-inch thick with the bottom of a glass.

Bake in the preheated oven until cookies just begin to brown on the bottom, 12 to 15 minutes. Allow cookies to cool on baking sheets for a few minutes before removing to a wire rack to cool completely.