Allow the chowder to cool down to room temperature before refrigerating. Transfer the leftover chowder to an airtight container and refrigerate for 2 to 3 days. If you can't consume the chowder within the recommended storage period, you can consider freezing it. Properly store the chowder in an airtight bag and freeze for 2 to 3 months. Thaw it in the refrigerator overnight before reheating.