A system and method for compartmentalizing micro-carriers in a bioreactor includes a container configured to store micro-carriers and a vessel configured to contain a fluid so as to prevent the micro-carriers from entering the vessel during sterilization, shipping, storage, or other pre-use handling of the system. One or more addition lines connect the container and the vessel such that the vessel is in fluid communication with the vessel. The one or more addition lines are contactable by at least one blocking element configured to reversibly block fluid flow between the container and the vessel. The container, addition lines, and vessel are configured to allow the micro-carriers to be injected into the vessel at any point during a cell culture run. The vessel may also include a rotatable wheel, a harvest port configured to allow for the removal of the micro-carriers from the vessel, and a media removal port comprising a retention screen for removing spent medium.