Start by preheating your oven to 400ºF and lining baking sheets with parchment paper. Thaw puff pastry in the fridge if frozen. This prep ensures smooth cooking.
Heat oil in a skillet over low heat, add onions and a pinch of salt, and cook slowly for 30 minutes. You want jammy, golden onions, not just soft sautéed ones.
Add mushrooms to the skillet and cook for about 5 minutes until tender. Combine them with the caramelized onions for the base of the filling.
Sauté apples with sugar in the same skillet until tender, around 10 minutes. Mix apples with the onions and mushrooms for a balanced sweet-savory flavor.
Stir in grated Gruyere, chives, and thyme. Season with salt and pepper to taste. This mixture will be the flavorful topping for your puff pastry.
Cut puff pastry into 2-inch squares and place on baking sheets. Brush with egg wash and top each square with a tablespoon of filling.
Bake at 400ºF for 25 minutes, rotating halfway. They’re done when puff pastry is golden and crisp. Let them cool slightly before serving.