Preheat the oven: Preheat your oven to 400°F (200°C) Lightly grease a baking dish that can fit the vegetables snugly in layers. (See note 3) Cook the onions: In a skillet/pot over medium heat, add 1 tablespoon of olive oil.
Add the diced onion and cook on low heat stirring occasionally, for about 10 minutes, or until soft and golden.
Spread the cooked onions in an even layer on the bottom of your greased baking dish.
Arrange the vegetables: Directly in the baking dish, alternate slices of butternut squash, red and green bell peppers, and potatoes in a snug, circular pattern on top of the onions until the dish is filled.
Season and brush the vegetables: In a small bowl, combine the remaining olive oil, minced garlic, thyme, salt, and pepper.
Use a brush to coat the arranged vegetables evenly with the mixture.
Bake: Cover the dish with foil and bake for 45 minutes, until the vegetables start to soften.
Remove the foil, and bake uncovered for an additional 15 minutes or until the vegetables are browned and tender.
After removing from the oven, let it sit on the countertop for a few minutes. This helps the vegetables finish cooking with the heat left in them (residual heat)