Preheat oven to 350 degrees F. Grease a 24 cup mini muffin pan with nonstick cooking spray. This recipe makes about 40 cookies, so if you have two muffin pans, grease them both. This will speed up the process.
Place the unwrapped peanut butter cups in the freezer until you are ready to use them.
In a medium bowl, whisk together the flour, salt and baking soda. Set aside.
In the bowl of a stand mixer, beat the butter, sugars, and peanut butter together until fluffy and smooth, about 3 minutes.
Beat in the egg, vanilla and milk. Add the flour mixture; mix until just combined.
Roll the cookie dough into balls, 1 tablespoon of dough per cookie. The dough will be a little sticky and that's ok. If it is too sticky, you can chill it in the fridge for 20 minutes. Place each ball into prepared muffin pans.
Bake for 8-10 minutes, don't over bake. Remove from oven. The centers will collapse a little and that is ok. Remove the peanut butter cups from the freezer and press a peanut butter cup into each cookie.
Place the pan in the refrigerator for 15-20 minutes so the cookies can cool. This will keep the peanut butter cups from melting and it will make the easier to remove from the pan.
When the cookies are completely cool, remove them from the pan and place on a cooling rack.