Preheat the oven to 350 degrees F. Add the milk, butter and salt to a medium saucepan and bring to a boil over medium heat. Add the all-purpose flour and almond flour; stir vigorously using a heat-proof spatula. Cook, stirring constantly, until a dense dough that pulls away from the side of the pot forms, about 3 minutes.
Transfer the dough to a stand mixer fitted with the paddle attachment and run briefly to cool a bit. Add 1 egg at a time, making sure the egg is fully incorporated before adding the next. Add the Gruyere, pepper and thyme; mix until just combined.
Using a 1-tablespoon scoop, drop the dough onto a parchment-lined cookie sheet. Top with a sprinkle of cheese. Bake until puffed up and browned in color, 30 to 40 minutes.