Preheat oven to 425℉. Pat chicken pieces very dry with a paper towel.
Heat a heavy, oven safe large skillet over medium high heat, add a drizzle of olive to coat the bottom of the pan. Add the zucchini, yellow squash, and onion. Saute until onions are translucent, squash is tender, and they have started to brown, about 5-8 minutes. Remove to a bowl and set aside. Add another drizzle of olive oil, followed by the chicken. Season chicken with a sprinkle of salt. Saute chicken, flipping occasionally, until golden brown on all sides and almost cooked through, about 5-8 minutes. Remove to a bowl and set aside.
Reduce heat to medium, add a drizzle of olive oil if needed, followed by the garlic, saute until garlic is translucent, about 1 minute. Add in the canned tomatoes, Italian seasoning, pesto, and a generous pinch of salt and pepper.
Using the back of a spoon or a potato masher, start breaking up the tomatoes until they integrate into the sauce. Simmer sauce for 15 to 20 minutes until reduced and thickened. When you pull a wooden spoon across the bottom of the pan, the sauce should spread back out very slowly.
Add the chicken back to the pan on top of the sauce, then place the zucchini mixture on top of the chicken, and sprinkle with the cheese.
Bake in the preheated oven for 15-20 minutes or until the cheese is melted and bubbly. Serve hot with quinoa, rice or pasta.