Melt the butter in a skillet over medium-low heat. Add the thinly sliced onion and cook for 18 to 20 minutes, stirring occasionally, until deeply golden and caramelized. Stir in the fresh thyme leaves during the last minute of cooking. Remove from heat and set aside to cool slightly.
Preheat your oven to 350F. Generously grease a 12-cup muffin tin with cooking spray or butter.
In a blender, combine the eggs, cream cheese, and heavy cream. Blend until completely smooth, about 20 to 30 seconds.
Pour the egg mixture into a large bowl. Add 3/4 cup of the shredded gruyere, the caramelized onions, salt, black pepper, and garlic powder. Stir until everything is evenly distributed.
Divide the mixture evenly among the 12 muffin cups. Top each egg bite with the remaining 1/4 cup of gruyere, pressing the cheese gently onto the surface so it melts into a beautiful golden crust.
Bake for 22 to 25 minutes, until puffed, golden on top, and set in the center.
Let the egg bites cool in the tin for 5 minutes before gently removing them with a spatula. Garnish with a few extra thyme leaves and serve warm.