Preheat oven to 400°F (200°C). Lightly coat the cut sides of the squash with half of the olive oil. Place cut side down on a baking sheet and roast for about 25-30 minutes, or until tender.
While the squash is roasting, cook the quinoa in vegetable broth according to package instructions.
In a skillet, heat the remaining olive oil over medium heat. Sauté the onion, bell pepper, and garlic until soft.
Combine the cooked quinoa, sautéed vegetables, cranberries, pecans, and thyme in a bowl. Season with salt and pepper.
Once the squash is done roasting, flip them over and fill each half with the quinoa mixture.
Return to the oven and bake for an additional 10-15 minutes. Serve warm.