Preheat your oven to 350°F (175°C) and arrange the mini phyllo shells on a large rimmed baking sheet.
In a large skillet, heat the olive oil over medium heat. Add the diced onion and sauté for 5 to 7 minutes until translucent and lightly golden.
Increase the heat to medium-high and add the chopped mushrooms. Cook, stirring occasionally, for 6 to 8 minutes until the mushrooms have released their moisture and turned deep brown.
Stir in the minced garlic, salt, black pepper, and fresh thyme. Cook for 1 minute until the garlic is fragrant, then remove the skillet from the heat.
Add the softened cream cheese and shredded Gruyère cheese to the mushroom mixture. Stir until the cheeses are melted and the mixture is well combined.
Spoon approximately 1 tablespoon of the mushroom filling into each phyllo shell, pressing down slightly to ensure they are full.
Bake for 8 to 10 minutes, or until the phyllo shells are crisp and the filling is heated through and bubbling.
Remove from the oven and let cool for 2 minutes. Garnish with fresh chives and serve warm.