In a small saucepan, over medium heat melt 1 stick of butter stirring it in the pan occasionally. The butter will foam as it cooks and will make popping noises. Keep a close eye on the butter once the popping slows down and stops. The butter will smell nutty and brown bits will appear at the bottom of the saucepan. Once the sizzling has stopped remove the butter from the stove and pour it into a small bowl to cool completely.
Spoon 3 tablespoons of the browned butter back into the saucepan and add the 3 tablespoons of organic brown sugar. Also, add the chopped pecans to the browned butter and sugar. Stir it together and cook over medium heat for 2-3 minutes. Remove the butter pecans from the saucepan and pour into a small bowl to cool completely.
In the bowl of a stand mixer, add the stick of softened butter and beat on medium speed for 1 minute. Then add in the brown sugar and cane sugar and beat on medium speed for 2 minutes. Add browned butter and beat on medium speed for 1 minute, until the mixture is smooth and fluffy.
Add the eggs to the mixture and beat on medium speed for 1 minute.
Add the flours, salt, and baking soda and beat on low speed just until everything is incorporated.
Remove the bowl from the stand mixer and use a rubber spatula to fold in the chocolate chips and butter pecans. Cover the bowl with plastic wrap and refrigerate it for at least 1 hour. The longer it chills the less the cookies will spread when it bakes.
Preheat the oven to 350°F and place the rack in the center of the oven. Line a baking sheet with a silicone liner. Scoop the dough into 3 tablespoon-sized balls onto the prepared baking sheets. Leave about 3 inches between the cookies so they will have room to spread.
Bake the cookies for 12-13 minutes, until they are golden brown. Remove them from the oven and allow them to cool on the baking sheet for at least 3-5 minutes before moving them to a cooling rack to cool completely.