Prepare the ingredients and heat the oven. Preheat the oven to 350°F. Cut the potatoes into uniform rounds approximately 1/8 inch thick. A mandoline or slicing blade may be used to maintain an even thickness. Finely mince the onion, grate or mince the garlic, chop the fresh thyme, and grate the Gruyère, keeping the 1/2-cup and 1-cup portions separate.

Cook the aromatics. Melt the butter in a saucepan over medium heat. Add the minced onion, garlic, and thyme. Gently sauté for 3–5 minutes, until the onion has softened and turned translucent without developing significant color.

Form the roux. Sprinkle the flour evenly over the softened aromatic mixture. Stir continuously and cook for 1 minute to remove the uncooked flour flavor.

Prepare the cream sauce. Gradually pour the milk into the saucepan while whisking continuously to keep the mixture smooth. Continue whisking for another 1–2 minutes, or until the sauce thickens sufficiently to coat the back of a spoon.

Add the cheese and seasonings. Remove the saucepan from the heat. Stir in 1/2 cup of shredded Gruyère along with the nutmeg, salt, and black pepper. Continue stirring until the cheese has completely melted and the sauce has a smooth, creamy consistency.

Begin assembling the gratin. Lightly butter a baking dish, then spread a thin coating of the prepared cheese sauce across the bottom. Arrange half of the sliced potatoes over the sauce in overlapping rows.

Complete the layers. Pour approximately half of the remaining sauce over the first potato layer. Arrange the rest of the potato slices on top in the same overlapping fashion, then distribute the remaining sauce evenly over the surface, allowing it to settle into the spaces between the potatoes.

Add the Gruyère topping. Scatter the remaining 1 cup of freshly grated Gruyère evenly over the assembled potato layers.

Bake the gratin. Transfer the dish to the preheated oven and bake at 350°F for 45–60 minutes. The gratin is ready when a knife passes easily through the potatoes and the cheese topping has developed a light golden-brown color.

Brown further if desired. For a more deeply caramelized surface, switch the oven to broil during the final 2–3 minutes. Monitor the gratin closely to prevent the cheese from burning.

Rest before serving. Remove the gratin from the oven and allow it to stand for 10 minutes. This brief resting period helps the layers settle and makes the gratin easier to portion while retaining its creamy texture.