Position a rack in the center of the oven and preheat to 375°F.
In a large pot filled halfway with boiling, lightly salted water, cook the potatoes for 3 minutes. Drain and spread them out evenly on a paper-towel-lined baking sheet to cool.
In a saucepan, melt the butter over medium heat. Add the chopped onion and cook, stirring, until softened, 3 minutes. Whisk in the flour for 2 minutes, then pour in half-and-half and bring to a boil, whisking constantly; cook for 1 minute. Remove from heat and stir in the cheese, 1 teaspoon salt and 1/2 teaspoon pepper. Let cool.