Preheat your oven to 375°F (190°C) to ensure even baking.
Gently clean the mushrooms with a damp paper towel and remove the stems, setting them aside.
In a large skillet, heat the olive oil over medium heat. Add the onion and sauté until translucent, about 3-4 minutes. Add the minced garlic and sauté for another minute.
Add the ground chicken or turkey, season with salt, pepper, thyme, and red pepper flakes. Cook until fully cooked, about 5-7 minutes.
Remove the skillet from heat, chop the reserved mushroom stems, and add them along with the Gruyere cheese. Mix until the cheese starts to melt into the filling.
Fill each mushroom cap generously with the chicken and cheese mixture. Place the stuffed mushrooms on a baking sheet lined with parchment paper.
Sprinkle breadcrumbs over the filled mushrooms for a crispy topping.
Bake in the preheated oven for about 20-25 minutes, until the mushrooms are tender and the tops are golden brown.
Remove from oven and let cool slightly before serving. Enjoy warm!