Place the 6 bone-in chicken thighs into a gallon-size zip-top bag and set aside.
In a medium bowl whisk together 4 tablespoons olive oil, minced garlic, thyme, juice of one lemon (about 3–4 tbsp), 1 teaspoon salt, 1/2 teaspoon pepper, and onion powder to form the marinade.
Pour the marinade into the bag with the chicken, seal the bag, and massage it with your hands until the thighs are evenly coated.
Refrigerate the chicken in the marinade for at least 30 minutes (up to 12 hours is fine).
While the chicken marinates, chop the yellow squash (or zucchini), bell peppers, red onion, and slice the mushrooms into bite-sized pieces and place them in a large bowl.
Toss the vegetables with 1 tablespoon olive oil, 1/2 teaspoon salt, and 1/4 teaspoon pepper until evenly coated.
Preheat the oven to 375°F (190°C). Lightly oil or spray a baking sheet.
Arrange the marinated chicken thighs on the prepared baking sheet and bake for 20 minutes.
Remove the sheet from the oven, scatter the prepared vegetables around the chicken, then return to the oven and bake for an additional 25 minutes, or until the chicken reaches an internal temperature of 165°F and vegetables are tender.
Let the chicken rest briefly, then serve hot; garnish with additional fresh thyme or parsley if desired.