Pre-heat oven to 425 degrees.
Combine on a rimmed baking sheet the squash, carrots, apple, shallot, onion and thyme.
Drizzle the vegetable combination with olive oil and season with salt, pepper, cinnamon and cumin.
Bake for 55-60 minutes until butternut squash and carrots are softened.
Remove thyme sprigs and set aside to cool slightly before transferring to a blender or food processor.
Pulse the vegetable mixture to break down the larger pieces and then blend together until smooth. Once the mixture is fully combined, stream in ½ to 1 cup of the broth in while continuing to blend.
Transfer the butternut squash soup base to a stockpot and simmer to reheat, while whisking in the remaining broth and heavy cream until combined.
Serve hot, sprinkled with pepitas, fresh cracked pepper, and a side of crusty bread.