Preheat oven to 350º F. Heat oil to medium-high heat in a large non-stick pan or skillet. Add onion and cook 3-5 minutes, stirring often until softened. Stir in Italian sausage, salt and pepper. Cook 7–10 minutes more, breaking up meat as it cooks, until browned. Stir mushroom into pan, cook 5 minutes more. Remove from heat and cool slightly.
In a large bowl stir together spinach, cumin and all cheeses. Stir in sausage mixture until combined.
Place phyllo cups on a large foil lined baking sheet about 1 inch apart. Fill each with mixture, about a tablespoon in each to create a mounded top. Bake at least 20 minutes, until cheese is melted and cups are crispy. Bake in multiple sets depending on sheet size and serve right away.