Preheat the oven to 375°F (190°C). Line a baking sheet with parchment paper. Place the mushroom cups on the baking sheet.
Gently remove the stems from the mushrooms and chop them.
Heat 1 tablespoon of olive oil in a skillet over medium heat. Add the chopped mushroom stems, onion, and garlic. Sauté for 3-4 minutes until softened. Add the sausage, breaking it up as it cooks, until browned. Season with salt, pepper, and red pepper flakes if using.
Turn off the heat. Stir in the breadcrumbs, Parmesan cheese, parsley, and cream cheese. Mix until well combined.
Spoon the sausage mixture into each mushroom cap, packing it in tightly.
Drizzle the remaining olive oil over the stuffed mushrooms. Bake for 20-25 minutes, or until the mushrooms are tender and the tops are golden brown.
Let cool slightly before serving. Garnish with Parmesan cheese.