Cut the butternut squash in half lengthwise and scoop out the seeds. Lay each half, cut side up, on a baking sheet lined with aluminum foil. Arrange the carrots and onions around the squash.
Drizzle the olive oil over all the vegetables and sprinkle ½ teaspoon of salt evenly over the top.
Roast the vegetables in the preheated oven for approximately 1 hour and 15 minutes, or until the butternut squash is fork tender. You may need to remove the onions from the baking sheet sooner if they begin to burn.
Remove the vegetables from the oven. Scoop out the insides of the squash and add them to a blender, along with the carrots, onions, about 1 tablespoon fresh thyme leaves, chicken broth, and apple juice. Blend until smooth.
Pour the butternut squash mixture into a large pot along with the canned pumpkin, coconut milk, cinnamon, remaining teaspoon of salt, and pepper. Heat the soup on the stovetop over medium heat until hot, stirring until well combined.
Serve warm topped with pepitas, fresh thyme sprigs, or a side of fresh bread.
Notes
Make sure the butternut squash is completely tender before removing it from the oven. It should be easy to pierce with a fork and scoop from the skin.
Keep an eye on the onion while the vegetables roast. Depending on its size, it may be ready before the butternut squash and carrots.
Be sure to use unsweetened coconut milk rather than sweetened coconut milk. Full-fat coconut milk will give you the richest and creamiest soup.
Apple cider will give the soup a slightly more pronounced fall flavor, but regular apple juice works well too.
If the soup is thicker than you prefer, stir in a little additional chicken broth until it reaches your desired consistency.