Preheat the oven to 375ºF and spray a baking sheet with non-stick cooking spray.
Spread the butternut squash cubes, onion, and apple out on the greased baking sheet.
Cut the end of the garlic head (opposite the root) so that the garlic cloves are exposed but remain intact. Set the garlic head open side up on the baking sheet.
Drizzle the olive oil over the vegetable mixture and garlic.
In a separate small bowl, mix together the cinnamon, nutmeg, salt, and pepper.
Sprinkle the spice mixture over all of the ingredients and massage the spices into all the ingredients.
Place the baking sheet in the oven and bake for 30 minutes.
Toss all the ingredients and flip the garlic head over so the open side faces down and bake for an additional 10-15 minutes or until the butternut squash is fork tender and begins to carmelize.
Remove the baking sheet from the oven and let the ingredients cool for 10 minutes.
When the garlic head is cool, squeeze the garlic cloves out of the garlic paper and into a high speed blender.
Add the butternut squash, onion, and apple to the blender.
Pour the broth into the blender and blend until smooth.*
Pour the soup into a sauce pan and add the sprigs of thyme to the soup and stir.
Heat the soup over medium heat for 10-15 minutes or until it reaches the desired temperature.
When the soup is ready to serve, remove the stems of fresh thyme from the pot, drizzle the top of the soup with creme fraiche, and top with freshly cracked pepper.
Serve and enjoy!