Preheat oven to 350°. Spray a rimmed baking sheet with cooking spray.
In a small sauté pan, heat oil over medium heat. Add onion and garlic; cook until fragrant, approximately 30 seconds. Add tomatoes, chopped basil, oregano, salt, and pepper, stirring well. Reduce heat, and simmer until thickened, approximately 5 minutes, stirring occasionally and mashing tomatoes with a potato masher. Transfer tomato sauce to a heatproof bowl.
Spoon 1 tablespoon tomato sauce and ½ tablespoon cheese into each phyllo cup. Place phyllo cups on prepared baking sheet.
Bake until cheese melts, approximately 3 minutes.
Garnish with basil, if desired. Serve immediately.
Recipe by TeaTime Magazine at https://teatimemagazine.com/pizza-phyllo-cups/