Preheat oven to 400°F (200°C).
Toss butternut squash and sweet potatoes with 1 tablespoon olive oil.
Spread vegetables on a baking tray and roast for 25 minutes until tender.
Heat remaining olive oil in a large soup pot over medium heat.
Add chopped onion and sauté until soft and translucent.
Stir in garlic, cumin, smoked paprika, and chili flakes.
Add roasted vegetables and vegetable broth to the pot.
Bring soup to a boil, then reduce heat and simmer for 10 minutes.
Blend the soup until smooth using a blender or immersion blender.
Stir in coconut milk, lime juice, salt, and black pepper.
Adjust seasoning and serve hot.