Preheat oven to 350°F and line a baking sheet with parchment paper.
In a large bowl, mix together fresh milled flour, baking powder, baking soda, and salt. Set aside.
In the bowl of a stand mixer, mix together softened butter, sugar, and vanilla for 2-3 minutes until fluffy and well combined.
Add the eggs one at a time mixing until just combined.
Add the dry ingredients in thirds mixing until the dough comes together and then pour in the chocolate chips.
Mix together and then use a cookie scoop or large spoon to drop the cookies on the prepared baking sheet. Be sure to leave 2 inces beween cookies allowing room to spread.
Bake for 12 minutes and add flaky salt right after taking them out of the oven.
Allow the cookies to cool on the pan for 4-5 minutes before transfering to a wire rack to cool completely.