Preheat your oven to 375°F (190°C). Generously grease a standard 12-cup muffin tin with non-stick spray or olive oil; place it on a large baking sheet. Organize all ingredients (cheese, sauce, chopped toppings) in separate bowls.
Separate 16 biscuits from the 2 cans of refrigerated flaky layer biscuit dough. Flatten each biscuit into a rough 4-inch circle, about ¼ to ⅛ inch thick in the center with slightly thicker edges.
Carefully press each flattened biscuit into a prepared muffin cup, lining the bottom and sides with a slight overhang to form a cup.
Add approximately 1 tablespoon of pizza or marinara sauce to the bottom of each dough-lined muffin cup. Sprinkle about 1 tablespoon of shredded mozzarella cheese over the sauce.
Evenly distribute your finely chopped and prepared toppings (e.g., mini pepperoni, bell peppers, red onion, black olives) among all 16 cups. Ensure any high-moisture vegetables or meat toppings are fully cooked and drained before adding.
Top each cupcake with another generous sprinkle of shredded mozzarella cheese. Add a tiny dusting of grated Parmesan (if using) over the mozzarella.
Carefully transfer the filled muffin tin(s) to the preheated oven. Bake for approximately 15-20 minutes, or until the biscuit dough edges are beautifully golden brown, and the cheese is gloriously bubbly and has developed some appealing golden-brown spots. Rotate the tin halfway through baking if browning unevenly.
Once baked, remove the muffin tin from the oven and let the pizza cupcakes rest in the tin for about 5 minutes. This allows the cheese and toppings to set slightly. Use a small offset spatula or butter knife to gently loosen the edges of each pizza cupcake, then carefully lift them out and transfer them to a wire cooling rack.
For a final touch, sprinkle finely chopped fresh basil (if using) over your warm pizza cupcakes. A final dusting of grated Parmesan or red pepper flakes can also be added. Serve warm and enjoy!