Preheat your oven to 400 degrees Fahrenheit and line a large baking sheet with parchment paper.
Toss the cubed butternut squash, chopped apple, and onion with olive oil, sea salt, and black pepper on the prepared sheet.
Roast the vegetable mixture for 25 to 30 minutes until everything is fork-tender and slightly caramelized.
While the vegetables roast, season the chicken breast with a pinch of salt and pepper, then bake or pan-sear until fully cooked to 165 degrees Fahrenheit.
Shred or finely dice the cooked chicken breast and set it aside to use as a high-protein topping.
Transfer the roasted squash, apple, and onion to a high-speed blender along with the chicken bone broth and ground cinnamon.
Blend on high until the soup is completely smooth and velvety, then pour it into a small pot over low heat.
Whisk in the Greek yogurt and dried thyme until the soup is warmed through, then serve in a bowl topped with the prepared chicken.