Dr. Gourmet Says... You should be safe to keep your baked Macaroni and Cheese in a tightly covered container in the refrigerator for about 48 to 72 hours. Let it cool, uncovered, for about 10 or 15 minutes before covering it and putting it in the fridge.It will be safe to keep it frozen for about 2 months.r. Gourmet Says... You should be safe to keep your baked Macaroni and Cheese in a tightly covered container in the refrigerator for about 48 to 72 hours. Let it cool, uncovered, for about 10 or 15 minutes before covering it and putting it in the fridge. It will be safe to keep it frozen for about 2 months.