Bring a large pot of salted water to a boil. Add the whole wheat pasta and cook according to package instructions until al dente. Drain the pasta in a colander and set aside.
While the pasta cooks, heat olive oil in a large skillet over medium heat. Add the diced zucchini and bell pepper, sautéing for about 5 minutes until they start to soften. Toss in the halved cherry tomatoes and chopped spinach, cooking for another 2-3 minutes until the spinach wilts and the tomatoes release their juices. Season with salt and pepper to taste.
In a large bowl or the skillet itself, mix together the cooked pasta, sautéed vegetables, and pesto. Stir gently to coat everything evenly, ensuring every bite will be packed with flavor.
Preheat your oven to 375°F (190°C). Transfer the pesto pasta mixture into your baking dish. Sprinkle the shredded mozzarella evenly over the top, followed by the grated Parmesan. This cheesy layer will create that irresistible golden crust.
Bake the pasta for 20-25 minutes, or until the cheese is bubbling and lightly browned. Remove from the oven and let it cool slightly before serving. Garnish with fresh basil leaves for a fragrant and colorful finish.