Preheat the oven to 375°F. Grease a 12-cup muffin pan with cooking spray.
Lightly flour your work surface, then roll out the pizza dough until it is a 14x8-inch rectangle. Using a sharp knife or pizza wheel, cut the dough into 12 even squares.
Arrange a pizza dough square inside each muffin cup. Divide the sauce equally among the cups, then alternately layer the cheese and toppings.
Bake the pizza cups for 18 to 22 minutes, or until golden brown and bubbling.
Remove the pizza cups from the oven, then garnish with dried oregano, Parmesan and crushed red pepper flakes (optional). Serve warm.
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