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. Drain and set aside.
While the pasta cooks, heat olive oil in a large skillet over medium heat.
Add the minced garlic and diced onion to the skillet and sauté for 2-3 minutes until fragrant and translucent.
Add the diced zucchini and red bell pepper to the skillet. Cook for 5-6 minutes, stirring occasionally, until the vegetables are tender.
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 the tomatoes soften.
Add the cooked spaghetti to the skillet with the vegetables. Toss well to combine and heat through for 1-2 minutes.
Remove from heat and stir in the chopped fresh parsley and fresh lemon juice.
Serve immediately, dividing the pasta evenly among four plates.