First, add the butter and sugar to the bowl of a stand mixer. Beat until combined and slightly fluffy, about 2 minutes.
Then, add in the eggs and vanilla. Stir until just combined. Do not overmix at this stage.
Mix in the flour, peanut butter, baking soda, and salt. Stir together until a thick dough forms. The dough will be very thick and slightly tacky.
Fold in the dark chocolate chips by hand using a spatula or wooden spoon. The chocolate should be evenly distributed.
Divide the batter into 6 huge balls of dough. Each ball will be roughly the size of a tennis ball.
Flatten each dough ball and place a peanut butter cup in the middle of the flattened disc. Fold up the sides of each dough ball, fully enclosing the chocolate square inside.
Place the 6 filled dough balls into an 8-inch round pan or pie plate. They should touch slightly, creating a pull-apart effect.
Place the pan in the freezer for 30 minutes. This step helps the cookies hold their shape while baking. After freezing, preheat your oven to 350 degrees Fahrenheit.
Bake for 18 to 21 minutes, or until the tops of the dough balls are just slightly golden brown. Remember, these will be gooey in the center on purpose.
Finally, remove from the oven and let them cool for about 5 minutes before digging in. The molten peanut butter cup center will be extremely hot, so be careful.