Preheat oven to 450 degrees F. Coat a 9x13 baking dish with nonstick spray.
Halve each zucchini lengthwise. Using a spoon, remove the flesh and finely chop it up. Place zucchini shells in the baking dish.
Warm olive oil in a medium skillet over medium-high heat. Add in the chopped zucchini and onion; saute until soft about 3-5 minutes. Stir in the garlic and cook until fragrant, about 30 seconds. Season with a pinch of salt and pepper.
Transfer mixture to a medium bowl and add in the marinara, ricotta, Parmesan, 3/4 cup mozzarella, and the Italian seasoning. Stir well to combine, and season with salt and pepper, to taste.
Divide mixture among the zucchini shells. Sprinkle with remaining 1/2 cup mozzarella and top with the mini pepperoni.
Bake until zucchini is tender and the cheese is golden brown, 20-30 minutes.
Garnish with freshly grated Parmesan and fresh basil before serving.