Heat coconut oil in a large pot over medium heat. Add chopped onion and cook until translucent, about 5 minutes. Add minced garlic and grated ginger, cooking for an additional 1-2 minutes until fragrant.
Stir in diced sweet potatoes and apples. Cook for another 5 minutes, stirring occasionally.
Add dried thyme, ground cinnamon, and salt. Stir to coat the vegetables and apples in the spices.
Pour in bone broth and bring to a boil. Reduce heat to a simmer and cook until the sweet potatoes and apples are tender, about 20-25 minutes.
Using an immersion blender, blend the soup until smooth and creamy. Alternatively, carefully transfer the soup in batches to a blender and blend until smooth.
Return the blended soup to the pot (if using a traditional blender) and stir in coconut milk. Heat gently until warmed through, but do not boil.
Taste and adjust salt as needed.
Ladle the soup into bowls and garnish with chopped fresh chives.