Preheat the oven to 400ºF. Slice the squash in half and scoop out the seeds. Arrange the squash on a large baking sheet cut-side-up, and sprinkle each have generously with salt and pepper. Bake the squash until tender and easily pierced with a fork, about 45 minutes.
While the squash is cooking, heat the olive oil in a skillet over medium heat and sauté the onion and celery until it starts to soften, about 5 minutes. Add in the garlic, sage, and thyme, and sauté one more minute, just until fragrant.
Add in the mushrooms, quinoa, and water, and bring the water to a boil. Once boiling, cover the pan with a lid and lower the heat, allowing the quinoa to cook until tender, and the water is absorbed, about 15 minutes.
Remove the stuffing from the heat and stir in the chopped pecans and dried cranberries, if using. When the squash is tender, fill each half with a heaping scoop of stuffing and serve warm. Season with black pepper, if desired.
If you have any leftovers, I prefer to store them separately for easier reheating later. To reheat, warm the squash in the oven for 15 minutes at 350ºF, and while that is heating stir the quinoa in a skillet over medium heat until heated through.