Warm the olive oil in a 4-quart soup pot over low heat. Stir in the onion, salt, and pepper. Cover the pot and let the onions sweat until they soften -- 5-8 minutes.
Stir in the beets, potato, vegetable stock and thyme. Bring to a boil over high heat. Then lower the heat, cover the pot, and let simmer until the potatoes are beets are definitely tender -- about 30 minutes. Cool for 15 minutes.
Ladle the cooled soup into the jar of an electric blender, and then add the juice of 1 lemon. Blend at high speed until the ingredients are smoothly pureed -- about 30 seconds. Taste carefully for seasonings -- you might like to add more salt.
If you are not going to serve the soup right away, allow it to cool completely. Then cover and refrigerate for up to 3 days. For longer storage, freeze the soup.
Serve the soup hot, warm, or cold, and garnish, if you wish, with a dollop or swirl of sour cream.