Cook your squash however you like, but you must cool it properly for safe storage. Rather than setting the squash out to cool on the countertop when cooking is finished, clear out space in your refrigerator and put the squash directly into the fridge. Set it on a hot pad or trivet on the refrigerator shelf with plenty of space on all sides so you don't warm up your other foods. In particular, don't set it below or directly next to dairy products. The squash must drop from above 140 degrees to below 40 degrees in approximately 40 minutes or less to prevent bacteria growth. Cut whole squash into pieces for faster cooling, and spread thick squash casseroles or soups out so they are less than 2 inches deep in their pans.

After the squash cools to below 40 degrees, cover it tightly with plastic wrap or place it in a tightly lidded container. Squash has a high water content and can dry out quickly if not covered. It also absorbs flavors around it, which is a great asset in cooking, but less of a benefit in the fridge, where it can pick up unwanted flavors from other dishes or ingredients it is stored near.

Before serving your squash, reheat it in the oven or on the stovetop until the internal temperature reaches 165 degrees. You can also microwave your precooked squash, but this can result in a rubbery texture and uneven heating, leading to unpleasant cold spots. If you do choose to microwave, cover the squash with waxed paper or a paper towel and stir it halfway through the cooking time, if it is a stirrable dish. As with more traditional reheating methods, heat it until the squash is 165 degrees at its center.

Even with tight covering, water can be pulled out of the squash during storage. In this case, you may see a puddle resting on the top of your squash dish, under its wrapping. Stir the water back in if it's a soup or other stirrable dish. Drain it off and pat the squash dry with a clean white paper towel if you can't stir it in, or if it doesn't reabsorb or dry off when you reheat the squash before serving.