Cook the penne pasta according to package instructions until al dente. Drain and set aside, reserving 1/2 cup of pasta water.
In a large skillet, heat the olive oil over medium heat. Add the diced onion and sauté for about 3 minutes until it becomes translucent.
Stir in the minced garlic and cook for an additional 1 minute until fragrant.
Add the zucchini, yellow squash, and red bell pepper to the skillet. Sauté for 5-7 minutes until the vegetables are tender but still crisp.
Stir in the cherry tomatoes and fresh spinach, cooking for another 2-3 minutes until the spinach wilts.
Add the cooked penne pasta to the skillet, along with the reserved pasta water, dried basil, oregano, salt, and pepper. Toss everything together until well combined and heated through.
Remove from heat and sprinkle with grated Parmesan cheese. Toss again to combine.
Serve immediately, garnished with fresh basil leaves if desired.