
Preheat the oven to 425°F and line a baking sheet with parchment. Cut the squash in half lengthwise and scoop out seeds. Make a few shallow diagonal cuts in the flesh. Drizzle with 1 tablespoon olive oil and season with ½ teaspoon salt and ¼ teaspoon pepper. Place cut-side up on the baking sheet and roast 45–55 minutes, or until tender and lightly caramelized.
While the squash roasts, heat remaining olive oil in a skillet over medium heat. Sauté the onion and apple until softened, 8–10 minutes.
Stir in spinach, pecans, quinoa, feta, cranberries, thyme, cumin, nutmeg, and remaining salt and pepper. Mix until well combined.
When squash is done, use a spoon to scoop a small amount of flesh from the top portion (above the seeds) to create a cavity for the filling. Chop the scooped squash and add it to the skillet with the onion and apple.
Spoon filling evenly into the squash cavities. Return to the oven for 10 minutes to warm through. Serve as is.