Meanwhile, stuff the pretzels. Cut a 1 ounce chunk of pizza dough and flatten slightly. Place a small piece of cheese in the center. Wrap the cheese completely with the dough, pinching the dough to seal the edges.
Drop a few pretzel bites at a time into the water, and allow to boil for about 10-15 seconds. Use a slotted spoon to remove them, allowing any excess water to drip off before placing them on the lined baking sheet.