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Preheat oven to 350 degrees. Line 2 cookie sheets with parchment paper or a silicon liner.
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In a heavy bottomed sauce pan, melt butter until browned. It takes about 5 minutes for butter to begin to smell nutty and start to brown, but watch carefully because it goes from perfectly browned to burned very fast.
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Once browned, remove from heat and allow to cool for 5 minutes.
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Combine flours, baking soda, and salt in a large bowl; set aside.
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Combine browned butter and sugars in the bowl of your mixer and mix until combined.
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Add eggs, one at a time, mixing thoroughly until combined.
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Stir in vanilla extract.
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With your mixer running on low, gradually add flour mixture; mixing until just combined. *if using chips or chunks, stir into dough now.
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Refrigerate dough for 30 minutes.
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Once dough has chilled, roll out into 1 inch balls.
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Place disks in the middle of the dough and press on top of the dough.
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Place on a cookie sheet 2 inches apart.
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Sprinkle balls with flaked sea salt (optional).
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Bake cookies for 12-14 minutes.
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Cool and serve.