Wait until after the first killing frost to dig up the calla lily tuber. Cut off the plant's frost-damaged foliage to within 1 to 2 inches of the soil.
Use a spading fork to dig up the calla lily rhizomes. Insert the spading fork into the soil 5 inches away from the plant, 3 inches deeper than the depth at which the bulb was planted. Use the fork to pry the bulb from the soil.
Inspect the calla lily rhizomes and discard any that have frost damage. These will be soft and mushy. Dust the soil from the remaining rhizomes, being careful not to damage them.
Set the calla rhizomes in a dry, warm area for three days, or until they are completely dry. This process is known as "curing."
Dust the rhizomes with fungicide powder. Wrap them in peat moss and store them in an area that remains dry, with temperatures between 50 and 55 degrees Fahrenheit.