Systems and methods for protected transportation of agricultural commodities are provided. The protected transportation is accomplished through the use of a thin, lightweight hermetic liner inside a shipping container. The liner is sealed at a first end and open at a second end, and the liner is positioned within the shipping container with the sealed first end at a back end of the shipping container and the second open end at a front, open end of the shipping container. A top portion of the liner is held to the ceiling of the shipping container via an attachment mechanism or via inflation of the liner and/or ribs in the liner. The bagged or bulk commodity is introduced through the open end and into the liner. The liner is then hermetically sealed, and the container is closed. After shipping, the agricultural commodity may be removed by unsealing the liner.