Preheat the oven to 425 degrees F. Line a baking sheet with a silicone baking mat or parchment paper.
In a medium saucepan, add 1 cup water, the butter and salt, and bring to a boil over high heat. Lower the heat to medium and add the flour all at once. Stir rapidly with a wooden spoon; the mixture will form a dough ball that will pull away from the sides of the pan. Continue to cook for a couple minutes.
Remove the pan from the heat and let cool for a couple of minutes. Stir so that the dough cools more evenly; you want the dough to be warm, but not so hot that when you start adding the eggs they cook as they hit the dough. In a mixer or by hand with a wooden spoon, add the eggs one at a time, stirring after each addition until the eggs are incorporated. The dough should become rather creamy. Stir in the grated cheese, bacon, thyme and a few grinds of pepper.
Spoon out small balls (about a heaping tablespoon) of the dough onto the baking sheet, with at least an inch separating the spoonfuls. Cook for 10 minutes; lower the heat to 350 degrees F and cook until puffed up and lightly golden, another 15 to 20 minutes.