Preheat the oven to 350 degrees. Coat a small baking dish with cooking spray.
Carefully cut the tops off of the tomato, making sure not to damage them, as they will act as the lid while baking.
Carefully scoop out the center flesh and seeds with a spoon, leaving the outer layer of the tomato all around to create a tomato bowl. (Keep the tomato insides for another recipe like tomato soup or discard).
Cook the orzo per package instructions then drain and reserve 1/4 cup of cooking liquid. (Side Note: For extra flavor, use chicken broth instead of water to cook the orzo).
While the orzo is cooking, heat the olive oil in a skillet over medium heat. Add the onion and cook, stirring often, for 2-3 minutes.
Add the mushrooms and cook, stirring occasionally, for 3 minutes. Add the minced garlic and crushed red pepper flakes and cook, stirring constantly, for 1 minute. Remove from the heat and season with sea salt and freshly cracked pepper, to taste.
Add the cooked and drained orzo to the onion and mushroom mixture along with a bit of the cooking liquid, if needed, and stir until well combined.
Add the parmesan cheese and mix well. Taste and season with sea salt and freshly cracked pepper, if needed.
Spoon the orzo into the tomato bowls evenly. Top with some mozzarella & a bit more Parmesan cheese then put the tomato lid on top.
Place the baking dish into the oven and bake for 30-35 minutes.
Remove and serve topped with fresh basil and extra parmesan cheese on the side. Enjoy!