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Add one stick of butter to a small skillet. Heat over medium flame until the crackling stops. Stir occasionally until the color starts to darken to a golden amber color. Once the butter has browned, remove from heat and pour into a small bowl off to the side. Be sure to scrape all the brown bits off the bottom of the skillet.
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Add remaining butter and granulated sugar to the bowl of an electric stand mixer fitted with the paddle attachment. Beat on medium/high until light and fluffy, about three minutes.
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Add the vanilla and molasses. Beat until combined, scraping down the sides as needed.
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Add the slightly cooled brown butter and brown sugar to the bowl. Beat on medium until combined.
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Scrape down the sides and add the eggs. Beat until combined.
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In a small separate mixing bowl, whisk together the flour, salt, and baking soda. Add all at once to the batter. Beat on low until almost combined. You still want to see some flour.
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Pour in the chocolate and M&M's. Mix on low until combined and no more flour is visible.
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Chill the dough for at least an hour in the refrigerator.
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Preheat the oven to 375 degrees F.
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Line a baking sheet with parchment paper. Using a large cookie scoop, scoop out the chilled dough. About six cookie dough balls per large baking sheet. Gently press down on the tops of the dough balls.
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Bake for 12-13 minutes until the edges start to turn golden brown. Let cool on the sheet for three minutes and then transfer to a wire rack to finish cooling.
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RECIPE ADAPTED FROM THE JOY THE BAKER COOKBOOK