Preheat oven to 400°F. Line a large baking sheet with parchment paper.
Wash and dry the zucchini. Slice each one in half lengthwise.
Use a spoon to scoop out the center of each zucchini half, creating a shallow boat shape. Leave about 1/4 inch of flesh around the edges. Reserve the scooped zucchini for another use.
Pat the inside of each zucchini boat dry with a paper towel. Season lightly with salt, pepper, garlic powder, and Italian seasoning.
Arrange the zucchini boats cut side up on the prepared baking sheet.
Spoon 2 tablespoons of marinara sauce into each boat and spread evenly.
Sprinkle mozzarella cheese generously over the sauce in each boat.
Top with pepperoni, olives, bell pepper, and mushrooms as desired.
Bake for 18 to 20 minutes, or until the zucchini is tender and the cheese is melted and bubbly with golden edges.
Remove from the oven and let cool for 2 minutes. Top with fresh basil and red pepper flakes if desired. Serve immediately.