To properly freeze cooked squash, let the cooked flesh cool for 10 minutes, scoop it out with a spoon, and pack it into freezer bags, storing horizontally. Alternatively, puree the squash before freezing for a ready-to-use product suitable for baked goods or soups.
Before freezing squash, roast it rather than boiling or steaming it to prevent excess water. To roast the squash, cut it in half and scoop out the seeds, saving them for roasting, if desired. Place the squash, cut side down, in a baking dish with 1/2-inch water. Bake at 400 degrees Fahrenheit for about an hour, until the flesh is completely cooked and the peels begin to brown. Allow the squash to cool, and then scoop out the flesh with a spoon.
When ready to freeze, pack the squash into freezer bags and store them horizontally to save space. Another option is to pack the squash into plastic storage containers, leaving one inch of head space. If freezing squash for use in baked goods, first puree the flesh in a food processor, or use a potato masher. Do not add water when pureeing to ensure that the squash is not too watery. To use the frozen squash in baked goods, thaw the puree and drain off any excess liquid. For soups, add the frozen squash directly to the pot.