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Start by freezing peanut butter cups. They should be frozen when they go into the oven.
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Preheat oven to 350 degrees and line baking sheets with parchment paper.
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In a large bowl, whisk together flour, salt and baking soda.
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In the bowl of a stand mixer, beat room temperature butter and sugar until combined.
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Add eggs and vanilla and continue stirring until well combined.
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Continue mixing and slowly add dry ingredients.
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Stir in chocolate chips.
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To layer cookies. Start with two tablespoons of cookie dough, place frozen peanut butter cup on top, then place another two tablespoons of cookie dough on top of the peanut butter cup.
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Gently seal the peanut butter cup inside the cookie dough by pinching the edges together.
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Press Peanut Butter M&M's onto top of cookie dough. I used eleven M&M's on each cookie.
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Bake at 350 degrees for about 15 minutes. Oven temperatures vary, so start checking before 15 minute mark.