Preheat the oven to 375°F and grease a mini muffin pan. Unwrap your peanut butter cups and place in the freezer (this make them easier to push into the cookies without melting).
In a medium mixing bowl, whisk the flour, salt, and baking soda.
In a large mixing bowl or the bowl of a stand mixer, add the butter, peanut butter, sugars, milk and vanilla. Add in the flour mixture and mix until just combined.
Place 1 tbsp balls of dough into each muffin pan divot (you will have around 2 dozen). Bake in the preheated oven for 7-9 minutes.
Immediately upon removing the cookies from the oven, remove the peanut butter cups from the freezer and press into the centers of the cookies.
Allow to cool completely before removing from the pan.