Meanwhile as the veggies roast, chop up half an onion. Add the onion and remaining avocado oil to a large soup pot over medium-low heat. Slowly caramelize the onions for 15-20 minutes, stirring often.
Crush the garlic and grate the ginger, add them to the pot and cook for about 3-5 minutes until they are soft and fragrant.
Add in broth, cut apple, fennel seed, red pepper flakes, remaining salt and pepper and roasted veggies. Cook the soup for about 15 minutes on medium heat until the flavours have mixed together, stirring occasionally.
Blend the soup using an immersion blender or blender to desired consistency. You may need to add in additional broth if your butternut squash is large. Pour in apple cider vinegar, coconut milk and chopped sage leaves, blend again.
Serve warm with optional toppings - non-dairy yogurt, sauerkraut, pumpkin or hemp seeds.