In a large pot or Dutch oven, heat olive oil over medium heat. Add shallots and cook until softened, about 5 minutes. Add garlic and cook for another minute until fragrant.
Add butternut squash, apples, and vegetable broth to the pot. Bring to a boil, then reduce heat and simmer for 20-25 minutes, or until squash is tender.
Remove from heat and carefully blend with an immersion blender or transfer to a regular blender until smooth. Return to the pot.
Stir in nutmeg, salt, and pepper to taste. Simmer for another 5 minutes to allow flavors to meld.