Step 1

Preheat the oven to 375 degrees F (190 degrees C). Spray cups of two 12-cup mini muffin pans with nonstick cooking spray.

Step 2

Heat olive oil in a skillet over medium heat. Add onion and cook until the edges of the onion begin to brown and caramelize, about 3 minutes. Add mushrooms and garlic, and cook until mushrooms are soft, 3 to 4 minutes. Season with salt and pepper. Transfer vegetables to a paper towel-lined plate with a slotted spoon.

Step 3

Roll out puff pastry sheet into a horizontal rectangle on a large, lightly floured cutting board. Use a pizza slicer to cut pastry into 4 rows horizontally and 6 rows vertically so that you have 24 (2 1/2-inch) squares. Press each dough square into each mini muffin cup and prick with the tines of a fork.

Step 4

Divide mushroom mixture amongst pastry cups. Top with shredded Gruyere and Parmesan cheeses. Sprinkle with thyme.

Step 5

Bake in the preheated oven until the pastry is puffed up and the corners are golden brown, 14 to 16 minutes. Cool in the pans on a wire rack for 3 minutes before transferring the bites to a serving dish.