Preheat the oven to 350°. Slice the cookie dough into six 1-inch-thick slices, then quarter the slices. Lightly press one quarter in each cup of a mini-muffin pan. Bake until just set, 9 to 11 minutes.
While the dough is still warm, push a peanut butter cup into each cookie cup and let cool in the pan. When the cookies are cool, use a spoon to remove them.