If you are wondering how to store cooked spaghetti squash you can refrigerate it in a sealed container for about 2 to 3 days or freeze it for about 6 months in a freezer safe bag. Let it cool completely before freezing, and thaw before re-heating. If you only cook one half of the squash and need to store the other raw half wrap it tightly in plastic wrap and keep it in the fridge for up to 5 days.