Pre heat oven to 375F. Slice your onions thin. Remove the puff pastry and cream cheese from the refrigerator so it comes up to room temperature
While the oven is preheating cook your onions. Add the butter or olive oil to a pan and on high medium heat cook the onions about 20 minutes until caramelized. They should be a deep golden brown
Gently roll the puff pastry with a rolling pin so it's smooth but not thin. Lay both sheets on to the muffin pan covering all the holes but not overlapping. Cut off the excess dough
Using a second muffin pan push down on the dough to mold the dough into the cups. Use a knife or pizza slicer to remover the majority of the extra dough around the cups.
Add about 1 tsp cream cheese to each cup. Add a layer of mozzarella on top. Add about 1 tbsp of onions on top of each cup. These will shrink down slightly
Bake for 18-22 minutes until the puff pastry is golden brown. I highly suggest putting a second large sheet pan under the muffin tin pan because the cheese may melt of the edge of the pan and create smoke
Let the cups cool for 10 minutes before removing from the baking pan this helps crisp the bottom of the puff pastry
Serve with fresh thyme leaves sprinkles on top or chives, or a drizzle of balsamic reduction
