Bioprocess Bag Management Systems support the usage and handling of flexible containers for bulk intermediate reagents and solutions. This system provides an organized and systematic means of managing flexible bags. A rigid, puncture-resistant polycarbonate shell top and bottom forms a protective barrier around the bioprocess bag. This novel management system isolates and stabilizes the bag and tubing during transport, effectively addressing the rapidly expanding demand for single-use flexible systems in biotechnology and biopharmaceutical applications. The system facilitates easy handling and ensures integrity is maintained by minimizing bag and port movement during transportation. A front compartment provides useful storage for tubing and the interior is contoured to fit commercially available bags such as the Thermo Scientific Hyclone 5L and 20L LabtainerTM Bioprocess containers. Users can choose between a clear version for easy sample viewing and an opaque version to protect light-sensitive contents. With the ability to withstand temperatures from -80 to 121oC, these systems are suitable for frozen and autoclave applications. When assembled, units are stackable to save space, and when not in use, the shells are nestable and easy to store.