Embodiments described herein generally relate to methods and systems for configuring settings of a cell expansion system including a bioreactor. Through a user interface, a user may configure display settings, system settings, and settings associated with protocols for loading, growing and/or harvesting cells. In configuring settings for protocols and associated processes, a diagram view or window of the cell expansion system is displayed in embodiments. The diagram view displays the process settings as graphical user interface elements. Settings available for configuration are enabled for selection in the diagram view. The diagram view allows the user to visualize the settings available for task configuration and to configure enabled settings. Configured settings are stored and capable of retrieval for subsequent execution or modification of the applicable protocol.