Preheat oven to 375 degrees. Toss cubed butternut squash with 2 tablespoon olive oil and salt and freshly ground black pepper, to taste. Roast for 25-30 minutes or until tender. Keep warm.
Meanwhile, place the quinoa in a fine-mesh sieve and rinse under running tap water to remove the bitter outer coating known as saponin.
Combine the quinoa and water in a large saucepan. Add salt and black pepper to taste. Bring to a boil, reduce heat to medium and cook uncovered for 15-17 minutes.
After approximately 15 to 17 minutes the “germ” begins to appear and much of the water will have evaporated or been absorbed.
Cover and let stand off the heat for another 15 to 20 minutes.
Heat a nonstick skillet over medium-high heat. Add the almonds and lightly toast, 3-4 minutes or until lightly browned in places. Immediately transfer to a small plate so the nuts do not burn.
In the same nonstick skillet, heat remaining 2 tablespoons olive oil over medium heat. Add the onion, reduce heat to low and cook, stirring often or until onions are golden and tender, approximately 8-10 minutes.
Add the garlic and thyme and cook 30 seconds or until fragrant. Stir in lemon zest and juice.
Return squash and quinoa to the skillet. Add parsley and Parmesan cheese and toss well. Serve immediately.