Heat the coconut oil over medium-high and add the chopped onion. Saute, stirring occasionally, until onion turns brown, about 12 minutes. Add the garlic and continue cooking another 2 minutes. Transfer the onion and garlic to your slow cooker.
Add the remaining ingredients for the soup, except for the collagen peptides, to the slow cooker. Cook on low for 6 to 8 hours (or on high for 4 to 5 hours), or until butternut squash is soft and cooked through.
Transfer the soup to a blender along with the collagen peptides, and blend until completely smooth (this will likely need to be done in batches. Serve with a drizzle of olive oil (or coconut milk), chopped pistachios and pecans.