Bring a large pot of salted water to a boil. Add the whole wheat spaghetti and cook according to package instructions until al dente, about 8-10 minutes.
While the pasta cooks, heat olive oil in a large skillet over medium heat.
Add the minced garlic to the skillet and sauté for 1 minute until fragrant, stirring frequently to prevent burning.
Add the diced zucchini and yellow bell pepper to the skillet. Cook for 5-6 minutes, stirring occasionally, until the vegetables are tender.
Add the cherry tomatoes, dried oregano, dried basil, crushed red pepper flakes, salt, and black pepper to the skillet. Cook for another 3-4 minutes until the tomatoes soften.
Add the fresh spinach leaves to the skillet and cook for 1-2 minutes until wilted.
Drain the cooked pasta, reserving 1/4 cup of the pasta water.
Add the drained pasta to the skillet with the vegetables. Toss to combine, adding reserved pasta water a little at a time to loosen the sauce if needed.
Remove from heat and stir in the chopped fresh parsley.
Divide the pasta among four plates and sprinkle each serving with 1/2 tablespoon grated Parmesan cheese.