Preheat your oven to 400°F (200°C), then spread the cubed squash and sweet potatoes on a baking sheet. Drizzle with one tablespoon of olive oil, sprinkle with salt and pepper, and toss to coat evenly. Roast for about 25-30 minutes until tender and lightly caramelized.
While the vegetables are roasting, heat the remaining tablespoon of olive oil in a large heavy-bottomed pot over medium heat. Add the sliced onions and cook, stirring occasionally, until they turn a deep golden brown and smell sweet, about 10-12 minutes.
Add the fennel seeds to the onions and cook for another minute until fragrant, allowing the flavors to bloom.
Pour in the vegetable broth and bring it to a gentle simmer, scraping up any browned bits from the bottom of the pot to develop flavor.
Once the roasted squash and sweet potatoes are cool enough to handle, add them to the pot. Use a wooden spoon to stir everything together, breaking down the vegetables slightly as they heat through.
Simmer the stew for another 10-15 minutes, allowing the flavors to meld and the vegetables to become even softer.
Taste the stew and adjust seasoning with more salt and pepper as needed. If you prefer a smoother texture, use an immersion blender to blend the stew until creamy, or carefully transfer in batches to a regular blender.
Once seasoned and blended to your liking, let the stew rest for a couple of minutes. Serve hot, garnished with fresh thyme if desired.
