Preheat oven to 400°F. Grease or line 6 muffin tin wells.
Sauté shallots in 1 tbsp ghee over medium heat (1 min). Add mushrooms (3–4 mins), then spinach (1 min). Remove from heat and squeeze out moisture with a paper towel.
Whisk eggs, egg whites, almond milk, baking powder, remaining ghee, salt, and pepper until frothy.
Assemble: Divide veggie mix into muffin cups. Pour egg mixture over, filling each ⅔ full. Top with mozzarella.
Bake 20–25 mins until set. Serve warm or store in fridge/freezer for later.