Organization systems for surgical instruments and associated methods and systems are disclosed herein. In one embodiment, a surgical instrument organization system can be configured for use in a medical environment, and can include a flexible, sterile container having a lower portion. The container can include an attachment system configured to elastically couple one or more surgical instruments to the lower portion of the container. In some embodiments, the container can be carried by a portable base coupled to a platform via an adjustable support member.