Preheat your oven to 350 degrees F. and line a baking sheet with parchment paper.
In a medium bowl, whisk together flour, baking soda, baking powder, and sea salt and set aside.
Add the butter to a skillet or saucepan and heat on medium-high heat. Whisk while the butter is cooking and starts to turn brown and foamy.
Remove from the heat and pour the brown butter into a separate bowl.
Cool the butter down.
Once the butter is cooled down, whisk the butter, granulated sugar and brown sugar until light and fluffy. Scrape down the sides of the bowl to ensure even mixing.
Now add the vanilla extract and egg. Beat until everything is well combined.
Gradually mix in the dry ingredients, then fold in the chocolate chips and chopped pecans. Make sure not to overmix!
Wrap the dough in plastic wrap and chill in the fridge for at least 12 hours.
When ready to bake, take the dough out of the fridge and allow it to soften at room temperature for about 30 minutes or less (if your house is warm). Use a large cookie scoop to divide the dough into portions and place the balls on the prepared baking sheet.
Bake for about 10 minutes, or until the cookies are golden brown.
Take the cookies out of the oven and let them cool on the baking sheet for 5 minutes then transfer them to a wire rack to cool. Finish by sprinkling them with a pinch of flaky sea salt and additional pecan nuts.
Notes
Make sure you don't end up overbaking the cookies- they just need 10-12 minutes in the oven. Keep in mind that they will firm up as they cool down.
Use good quality and fresh leavening agents. Old leavening agents can lose their effectiveness, and your cookies will turn out dense and flat if you use them.
You can store these pecan brown butter cookies for 5-7 days in an airtight container at room temperature.
If you want them to last longer, you can also freeze them. Arrange them on a baking sheet and freeze them for 2 hours until they're solid, then transfer them to a freezer safe bag or container and back in again for up to 2 months.