Preheat the oven to 400ºF. Trim the ends of the squash and cut in half lengthwise. Scoop out the seeds.
Place in a baking dish, cut side up, and brush lightly with some of the olive oil. Sprinkle with salt and pepper and roast 15 to 20 minutes, until the flesh is soft and lightly browned. Set aside to cool.
Heat the remaining oil in a Dutch oven or large soup pot over medium heat. Add the prosciutto and sauté until crispy, about 3 minutes. Remove with a slotted spoon to a paper towel lined plate.
Add the onion to the pot, season with salt and pepper, and sauté until tender, 3 to 5 minutes. Add the garlic and thyme, and cook 1 minute more.
Scoop out the flesh of the squash into the pan and add the cauliflower. Stir in the broth and bring to a boil. Reduce the heat to a simmer and cook 15 minutes, until the cauliflower is tender.
Transfer the soup to a blender and blend until smooth (or use an immersion blender to blend). Return to the pot over low heat and add the parmesan cheese. Stir until the cheese is melted and the soup is warmed to your liking.
Serve with dollops of sour cream, and sprinkle with crispy prosciutto, fresh thyme leaves, and pepitas, as desired.
Notes
Storage Information: You can store your soup in an air tight container for up to a week in the refrigerator. You can also freeze it for up to 2 months.