In a large bowl, whisk together the melted butter and peanut butter until smooth. Add the brown sugar and granulated sugar and mix until fully combined. Add the eggs, egg yolk and vanilla and mix until smooth.
Stir in the flour, baking soda, baking powder and salt. Mix just until combined, being careful not to overmix.
In a medium-sized bowl, combine the mini chocolate chips, semi-sweet chocolate chips, mini M&M’s and regular M&M’s. Pour about half of the mixture into the cookie dough and use a spatula to gently fold them in.
Line a cookie sheet with parchment paper. Using a large 3 tbsp cookie scoop, scoop the dough into even cookie dough balls. Gently press the tops of each cookie dough ball into the remaining M&M and chocolate chip mixture, making sure the tops are completely loaded.
Cover and chill the cookie dough in the refrigerator for 30–45 minutes. Keep the dough refrigerated until you’re ready to bake each batch.
Preheat the oven to 350°F. Place about 5 cookie dough balls on the prepared cookie sheet, spacing them about 2 inches apart. Bake for 11–12 minutes, or until the edges are set and the centers still look slightly underbaked.
As soon as the cookies come out of the oven, place a large round cookie cutter or glass around each cookie and gently swirl it in a circular motion to reshape the cookies into perfect circles.
Let the cookies cool on the baking sheet for about 5 minutes before transferring them to a cooling rack to cool completely.