Heat a large pot on medium heat. Once hot, add the extra-virgin olive oil, chopped onion, garlic, salt, and sage leaves. Sauté until soft for around 5 minutes.
Add the cubed squash, chopped carrots, celery, ground black pepper, and ground nutmeg and stir for 30 seconds to a minute to give it time to absorb all the flavors. Then add the vegetable broth. Bring to a boil, then reduce the heat and let it simmer for about 10 to 15 minutes until the butternut squash is tender (check with a fork).
Remove from the heat, use an immersion blender, or pour the soup into a blender, and blend until smooth. Depending on how thick you like your soup, you can add an extra cup of broth, a bit at a time, and keep blending.
Taste and adjust for seasoning. If needed, reheat the soup in the pot until it’s hot and steamy. Serve in individual bowls, and top it with some sage leaves, pumpkin seeds, and fresh thyme.