Via specialized granaries. Granaries are a key part of the agricultural technological package. Their exact form will vary due to local materials, climate, and pests but generally in Europe you will find elevated structures, often built on mushroom-shaped pillars that restrict the entrance of rodents and insects. In England these are called "staddle stones". More conventional-looking construction might include rat-resistant mouldings or other features. Occasionally the upper floor of an existing space might be used. In conventional buildings or for smaller amounts of grain, wooden chests or pottery vessels might be used.

Edit: There is also a Mediterranean practice which is significantly different, involving subterranean silos. The forms and extent of these is better known as they are better preserved in the archaeological record, and there's a lot to be said on the subject, but someone else would need to do so as I'm not well-read on this tradition.