Preheat the oven to 375°F. Lightly spray a 12-cup muffin tin with cooking spray.
On a lightly floured surface, roll out the puff pastry dough slightly to smooth the seams. Cut into 12 equal squares and gently press each square into a muffin cup, letting the corners rise up slightly. Use a fork to prick the bottom of each square 2 to 3 times to prevent puffing.
In a large bowl, whisk the eggs until smooth. Using a pastry brush, lightly brush the edges of the puff pastry with some of the beaten eggs to help them brown evenly.
In the same bowl with the remaining eggs, add the half-and-half, Gruyère, ham, Dijon mustard, thyme, salt, and pepper. Whisk to combine.
Evenly divide the mixture among the puff pastry cups, filling each cavity about 3/4 full. Transfer to the oven and bake on the middle rack for 25 to 28 minutes or until puffed, golden, and set in the center.
Let cool slightly before removing from the pan. Serve warm or at room temperature.