Peel and chop the butternut squash into chunks.
Heat olive oil in a large pot over medium heat. Add onion and garlic; cook until soft, about 5 minutes.
Add squash cubes and stir for 2 minutes.
Pour in vegetable broth, bring to a boil, then simmer for 20–25 minutes until squash is tender.
Blend the soup until smooth using an immersion blender (or regular blender, carefully).
Stir in heavy cream, nutmeg, salt, pepper, and chili flakes (if using). Simmer for 5 minutes.
Taste and adjust seasoning as needed.
Serve hot with crusty bread.