Cut the zucchinis in half lengthwise and scoop out the center with a spoon, creating the boats. Set the scooped-out flesh aside.
In a skillet over medium heat, add olive oil. Sauté the chopped red onion and minced garlic for about 2-3 minutes until the onion is translucent.
Add the Italian sausage to the skillet, breaking it apart with a spatula. Cook until browned and fully cooked, about 5-7 minutes.
Stir in the cherry tomatoes, reserved zucchini flesh (chopped), oregano, basil, red pepper flakes, salt, and pepper. Cook for an additional 5 minutes until the tomatoes soften.
Remove the skillet from the heat and mix in half of the mozzarella cheese.
Place the zucchini boats in a baking dish, cut side up. Fill each boat generously with the sausage mixture.
Sprinkle the remaining mozzarella cheese on top of the stuffed zucchinis.
Cover the baking dish with foil and bake for 20 minutes. Then, remove the foil and bake for an additional 10-15 minutes until the cheese is bubbly and golden.
Remove from the oven, let cool slightly, and garnish with fresh basil leaves before serving.
Notes
Feel free to adjust the spice level by choosing mild or spicy sausage.