Place butternut pumpkin, onions, pears, tomatoes and carrot in a large roasting pan. Drizzle olive oil on top. Season with pepper and nutmeg.
Roast in the preheated oven until pumpkin is easily pierced with a knife, about 1 hour. Cool until pumpkin is easily handled, about 10 minutes.
Scoop flesh out of the pumpkin with a spoon; place in a pot. Discard peel. Transfer roasted onions, pears, tomatoes and carrot to the pot. Add 1 cup chicken stock. Puree mixture with an immersion blender until smooth.
Stir remaining 1 1/2 cups chicken stock into the pot. Heat soup until warmed through, about 10 minutes. Season with salt.
If you don't have an immersion blender, use a blender or food processor to blend the squash mixture in batches.