Heat oil in a soup pot over medium heat. Cook the onions, bell pepper, and garlic until tender and slightly browned.
Stir in the butternut squash, mushrooms, black pepper and half the salt. Cook and stir for 5 minutes. Pour the wine, and stir and scrape the bottom of the pot to get the brown bits.
Add the spinach, beans, honey, and water. Stir in the bay leaf, nutmeg, sage and remaining salt.
Increase heat to a low boil. Reduce heat and simmer until the butternut squash is tender and the liquid has reduced (about an hour). Stir occasionally while cooking.