When you pick the last of the crop, separate the tomatoes into three groups for storage: those that are mostly red, those that are just starting to turn, and those that are still green, Upham says. Don’t keep tomatoes that have defects such as rot or breaks in the skin. Place the tomatoes on cardboard trays or cartons, using newspaper to separate fruit if you stack them. The paper helps contain any juice that may ooze out. Store groups of tomatoes at as close to 55 degrees as possible until you need them, Upham says.