Preheat your oven to 400°F and line a large baking sheet with parchment paper.
Toss the cubed butternut squash, chopped apple, and diced onion with olive oil, sea salt, and black pepper on the prepared sheet.
Roast the vegetables for 25 to 30 minutes until the squash is fork-tender and slightly caramelized.
While the vegetables roast, poach the chicken breast in a small pot of simmering water until the internal temperature reaches 165°F, then shred it finely with two forks.
Transfer the roasted squash, apple, and onion to a high-speed blender and add the chicken bone broth, cinnamon, and nutmeg.
Blend on high until the soup reaches a silky, velvety consistency, adding a splash of water if a thinner soup is desired.
Pour the warm soup into a bowl and stir in the shredded chicken to incorporate before serving.