Place cubed potatoes into a glass dish, and cook in the microwave oven for 7 to 10 minutes, or until soft.
While the potatoes are cooking, melt the butter in a large pot over medium-high heat. Whisk in flour until smooth, then gradually stir in the milk. Bring to a boil, then reduce heat to medium, and simmer for 5 to 10 minutes, or until slightly thickened.
Stir in the potatoes and onion, and cook for 5 more minutes. Stir in the sour cream and Cheddar cheese until melted and well blended. Season with salt and pepper.