In a medium bowl, whisk together the flour, baking soda, cinnamon, salt, and nutmeg. Set aside.
In the bowl of a stand mixer, add the butter and beat 60 seconds. Add brown sugar and granulated sugar and beat until smooth, scraping down the sides with a spatula if necessary.
Add in the eggs and vanilla extract and beat until combined and smooth.
With the mixer off, add all of the dry ingredients. Turn the mixer on low and mix until just combined. Stir in the oats and pecans.
Scoop the cookie dough into round balls the size of a golf ball. Place on greased baking sheets, about 2-inches apart. Bake for 6 to 8 minutes or until the edges of the cookies are golden brown but the centers are soft. Remove from the oven and let the cookies cool on the baking sheet for 2 to 3 minutes. Transfer cookies to a wire cooling rack to cool completely.