Preheat your oven to 375°F (190°C). Clean the baby bella mushrooms gently with a damp paper towel. Carefully remove the stems, creating enough space to hold the filling. Finely chop the stems and set them aside for later.
In a large skillet, heat 1 tablespoon of olive oil over medium heat. Add the chopped sweet onion and sauté until it becomes translucent, about 4-5 minutes. Stir in the minced garlic and chopped mushroom stems, cooking for an additional 2-3 minutes until fragrant.
Add 16 ounces of lean ground chicken or turkey to the skillet. Season with salt, pepper, 1 teaspoon of dried thyme, and ½ teaspoon of red pepper flakes. Cook until the chicken is browned and cooked through, about 7-10 minutes.
Once the chicken is fully cooked, remove the skillet from heat. Stir in 4 ounces of grated Gruyere cheese until melted and well combined.
Using a spoon, fill each mushroom cap with the chicken and cheese mixture. Be generous, as these bites are meant to be packed with flavor. Place the stuffed mushrooms on a baking sheet.
Sprinkle 3 tablespoons of breadcrumbs over the stuffed mushrooms for a crunchy topping.
Place the baking sheet in the preheated oven and bake for 20-25 minutes, or until the mushrooms are tender and the tops are golden brown.