Pre-heat oven to 375°F. Heat coconut oil over medium heat in a large cast iron skillet and sauté onion until soft and translucent. Add garlic and mushrooms and cook until the mushroom moisture evaporates. Season with salt and pepper and spoon to a plate to cool to room temperature.
In a large bowl, beat the eggs with coconut milk, coconut flour, salt, and pepper until combined. Then, add the sautéed the mushrooms and spinach and stir to combine.
Brush the remainder of melted coconut oil onto a muffin tin. Spoon the egg mixture into the muffin tins and top with halved cherry tomatoes.
Bake in oven for 20 minutes, rotating the tray at the halfway point. Let muffins cool in the pan for a few minutes. Enjoy!