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Preheat the oven to 350*F and line two sheet pans with parchment paper.
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In a medium bowl, whisk together the pastry flour, salt and baking soda.
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In the bowl of a stand mixer fitted with a paddle attachment, beat the butter and sugar on medium speed until light and fluffy, scraping down the sides of the bowl as needed. Add the egg and beat on medium until completely incorporated. Add the peanut butter and vanilla and mix on medium until incorporated. Pour in half of the dry ingredients, mixing on low until just incorporated, then add the other half and do the same. Add both the milk and dark chocolate and mix on low speed until evenly distributed.
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With a large cookie scoop, or ice cream scoop, measure, scoop the dough onto the prepared baking sheets. Sprinkle the cookies lightly with big, flaky sea salt, if desired. I divide the cookies out by scooping 6 onto the first tray and 4 on the second, so they don't spread into each other while they bake.
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Bake the first tray for 14-17 minutes, rotating once during baking. When they're ready they should be lightly golden on the edges, but not fully browned. Remove from oven and place the baking sheet on a cooling rack, allowing the cookies to cool completely on the baking sheet. Repeat with the next sheet of cookies.
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If you want to double the recipe, this dough freezes really nicely once it's scooped.