Dig up the yacon rhizomes in the late fall after the plant's top-growth has died back. Separate the smaller reddish rhizomes from the larger, brown tubers. The reddish rhizomes usually appear at the base of the plant's stem. They are easily distinguishable from the brown tubers.
Place the yacon rhizomes in a tray or plastic container. Cover them with moist coconut fibers or sawdust.
Store the container of rhizomes in a root cellar or refrigerator. Keep the rhizomes in the dark. Maintain the temperature around the rhizomes at 40 degrees Fahrenheit.
Check the rhizomes once a month to make sure they are not rotting. Discard any rhizomes that show signs of rot. Remoisten the coconut fibers or sawdust, if necessary.