Preheat the oven to 375°F (190°C).
Lightly grease a mini muffin pan or line it with paper liners.
In a medium bowl, whisk together the flour, salt, and baking soda.
In a separate large bowl, beat the butter, granulated sugar, peanut butter, and brown sugar until light and fluffy.
Mix in the egg, vanilla extract, and milk until smooth.
Gradually add the dry ingredients and mix just until combined.
Roll the dough into 1-inch balls and place one in each muffin cup.
Bake for 8 minutes, or until the edges are lightly golden. Do not overbake.
Remove from the oven and immediately press one miniature peanut butter cup into the center of each cookie.
Allow the Peanut Butter Cup Cookies to cool in the pan for several minutes before carefully transferring them to a wire rack.