Heat oven to 300°F. Place squash cut-side down on a baking sheet. Bake for 20 to 25 minutes.
While squash is cooking, heat coconut oil in a large sauté pan over medium heat. Add onion and cook until translucent. Add spinach and cook for 2 minutes. Remove from heat and let cool.
Remove squash from oven. Remove squash threads and place in a bowl. Add spinach mixture and quinoa and mix together. Pour in egg mixture and stir to combine.
Transfer mixture to a shallow baking pan, spreading it evenly. Bake for 45 minutes.
Remove from oven. Let cool and slice into 2 pieces.