Preheat the oven to 400 degrees F (200 degrees C). Line a 13x18-inch, half-sheet pan with parchment paper.
Grate provolone and mozzarella cheeses with the larger side of a box grater into a large bowl. Use the smaller side and grate in Parmigiano-Reggiano cheese. Toss with your hands to combine.
Scoop tablespoonfuls of the cheese mixture into 12 circular piles on the prepared baking sheet, making sure you're getting all three cheeses in each scoop. Top each circle with about ¾ teaspoon pizza sauce, then place a slice of pepperoni on top.
Bake in the center of the preheated oven until melted and sizzling, 12 to 15 minutes.
Remove parchment paper and chips to a wire rack to cool. Line the baking sheet with a fresh sheet of parchment paper.
Repeat Steps 3 to 5 to bake remaining 18 chips.
Let chips cool to room temperature, 15 to 20 minutes. Remove from the parchment paper and serve.