Preheat the oven to 375°F.
Slice the zucchinis in half lengthwise and scoop out the center using a spoon, creating boats. Place the zucchini halves on a baking sheet.
In a skillet, heat the olive oil over medium heat. Add the diced mushrooms and sauté for about 5 minutes until they are soft.
Add the chopped spinach and cook for an additional 2-3 minutes until wilted. Remove from heat.
In a mixing bowl, combine the sautéed mushrooms and spinach with ricotta cheese, half of the mozzarella cheese, Parmesan cheese, garlic powder, onion powder, salt, pepper, and red pepper flakes. Mix until well combined.
Spoon the filling into each zucchini boat, packing it in gently. Sprinkle the remaining mozzarella cheese on top of the stuffed zucchinis.
Bake in the preheated oven for 25-30 minutes, or until the zucchini is tender and the cheese is bubbly and golden.
Remove from the oven and let cool for a few minutes. Garnish with fresh basil before serving.