In a mixing bowl, whisk together the flour, salt, and baking soda. Set aside.
Cream together the butter and peanut butter with a stand mixer or hand mixer. Add the brown sugar, sugar, and pudding mix and beat again. Add the eggs, one at a time, and mix to combine.
Add the peanut butter mixture to the flour mixture and stir until combined. Fold in the M&Ms and chocolate chips.
Use a 2 Tablespoon cookie scoop to measure the dough and place on a parchment paper lined baking sheet about two inches apart. Bake the cookies at 375 for 8-10 minutes.
After removing from the oven, allow the cookies to rest on the baking for 5 minutes before transferring to a cooling rack.