Preheat oven to 375°F (190°C). Clean mushrooms by wiping caps with a damp paper towel; avoid rinsing. Gently twist or cut out stems and set caps aside on a baking sheet lined with parchment, cavity side up.

Lightly season the inside of each mushroom cap with a small pinch of kosher salt and a grind of black pepper. Brush the outside of the caps with about 1 tablespoon olive oil to help browning.

Filling

Cook aromatics and stems

Finely chop the reserved mushroom stems. In a medium skillet over medium heat, melt 2 tablespoons butter with 1 tablespoon olive oil. Add the chopped stems and 1/2 cup finely diced onion. Cook, stirring occasionally, until softened and any released liquid has evaporated, 6–8 minutes.

Add 3 minced garlic cloves and 1 tablespoon fresh thyme leaves (or 1/2 tsp dried). Cook 30–60 seconds until fragrant, being careful not to brown the garlic.

Combine filling

Transfer the cooked mixture to a bowl and let cool 2–3 minutes. Add 4 ounces softened cream cheese, 1/2 cup grated Parmesan, 1/2 cup Panko breadcrumbs, 2 tablespoons chopped parsley, 1/4 teaspoon ground black pepper, and optional 1/8 teaspoon crushed red pepper flakes. Mix thoroughly until well combined. Taste and adjust salt (add up to 1/4 tsp kosher salt if needed). The mixture should be moist but hold its shape; if too wet, add up to 1–2 tablespoons more Panko.

Assembly & Baking

Stuff mushrooms

Using a small spoon or piping bag, mound about 1 to 1 1/2 tablespoons of filling into each mushroom cap, pressing gently so it stays in place. The caps should be generously filled but not overflowing.

Place filled mushrooms on the prepared baking sheet. If using the optional topping, combine 2 tablespoons extra Parmesan with 2 tablespoons panko and sprinkle a pinch over each stuffed mushroom.

Bake

Bake in the preheated 375°F (190°C) oven until filling is golden and mushrooms are tender, 18–22 minutes. For a browned top, switch to broil on high for 1–2 minutes, watching closely to avoid burning.

Remove from oven and let rest 3–4 minutes. Garnish with 1 tablespoon chopped parsley. Serve warm.