Brown the butter: Melt butter in a light-colored saucepan over medium-low heat, swirling occasionally, until the milk solids turn golden and the butter smells nutty. Remove from heat immediately and pour into a mixing bowl. Allow to cool until softened but not melted.
Cream the wet ingredients: In a large bowl of a stand mixer, (or use a large bowl and hand mixer) cream together the cooled brown butter, white sugar, and brown sugar until combined. Add eggs one at a time, mixing well after each. Add vanilla and mix to combine.
Mix the dry ingredients: In a separate bowl, whisk together the fresh milled flours, baking powder, baking soda, and salt.
Combine: Add the dry ingredients to the wet ingredients and mix until just combined. Do not overmix.
Let the dough rest. Fresh milled flour needs a little time to fully absorb moisture. After mixing, let the dough sit for at least 15 minutes before scooping — this is called autolyse, and it makes a noticeable difference in texture. Don’t skip it.
Fold. After the autolyse period, fold in the chocolate chips.
Bake: Drop by rounded spoonfuls (or use a cookie scoop) onto a parchment-lined baking sheet. Bake at 425°F for 7 minutes, then drop the temperature to 375°F for 6-8 minutes or until the edges are golden brown. Centers will look slightly underdone — that’s perfect. Let cool on the pan for 5 minutes before transferring to a cooling rack.