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 avoid burning.
Add the diced zucchini and red bell pepper to the skillet. Cook for 5 minutes, stirring occasionally, until vegetables begin to soften.
Stir in the cherry tomatoes, chopped spinach, dried oregano, dried basil, crushed red pepper flakes, salt, and black pepper. Cook for an additional 3-4 minutes until the spinach wilts and tomatoes soften.
Drain the cooked pasta, reserving 1/4 cup of 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 sprinkle grated Parmesan cheese over the pasta. Toss gently to incorporate the cheese.
Divide the pasta evenly among four plates and serve immediately.