Combine onion, vinegar, sugar, cinnamon stick, peppercorns and cloves in a large saucepan. Bring to a boil over medium-high heat. Cover, reduce heat to medium-low and simmer until the onion is tender-crisp, 4 to 6 minutes. Stir in beets. Transfer to a large bowl and let marinate, stirring occasionally, for 30 minutes.