Preheat oven to 400° F. Spray 9x13 glass dish with nonstick cooking spray and set aside.
Grate zucchini and measure out 4 cups. Sprinkle salt over zucchini and let sit for 10 minutes.
Using a tea towel, ring out zucchini to remove any excess water. Place in a bowl and mix with black pepper, eggs, 1 cup mozzarella cheese, 1 cup cheddar cheese, and parmesan cheese. Stir to combine well.
Spread zucchini mixture evenly into prepared baking dish and bake for 20 minutes.
Remove from oven and top with pizza sauce, remaining mozzarella cheese, pepperoni, and any desired pizza toppings.
Bake 15 more minutes and remove from oven. Garnish with fresh basil. Cool 5 minutes before cutting and serving.