Embodiments described herein generally relate to methods and systems for using an air removal chamber as a control for a process in a cell expansion system. The air removal chamber may be mounted on a fluid conveyance assembly for use with the system. Fluid is pumped into a fluid containment chamber of the air removal chamber, in which the level of fluid in the fluid containment chamber may be monitored through the use of one or more sensors. The sensors are capable of detecting air, a lack of fluid, fluid, and/or a gas/fluid interface, e.g., an air/fluid interface, at measuring positions within the air removal chamber. Protocols for use with the system may include one or more stop conditions. In an embodiment, the stopping of a process is automated based on the detection of air, a lack of fluid, and/or a gas/fluid interface in the air removal chamber.