Preheat the oven to 375°F.
Heat and drizzle oil in a large, heavy skillet set over medium heat. Sauté the butternut squash for 2-3 minutes until the squash is starting to turn golden. Add tomatoes and garlic to the pan and cook for another 2 minutes, until the tomatoes release their juices. Add the fonio and cook for about 5 minutes. Add the spinach and cook until it wilts.
Meanwhile, stir together the eggs, milk, cheese, salt, and pepper in a medium bowl. Place the fonio and vegetable mixture into a baking dish or regular sized muffin tins that have been sprayed with nonstick spray, and pour the beaten eggs over top. If you like, sprinkle with more grated or crumbled cheese.
Bake for 15-20 minutes, until puffed and set. Serve warm, at room temperature, or cold.