Systems for limiting pressure differences in dual compressor chillers are provided. To achieve the efficiency benefits of series flow chillers within a single unit, an evaporator and/or a condenser may be partitioned into separate chambers by a baffle. Process fluid may then flow through one chamber of the evaporator and/or condenser prior to entering the other. This configuration creates a pressure differential between chambers which may reduce compressor head and result in greater chiller efficiency. However, to maintain the structural integrity of the evaporator and/or condenser baffle, a system for limiting this pressure differential may be employed. This system may include an evaporator pressure equalization valve, a common liquid line, or an equalizing line between separate liquid lines. Methods of operating dual compressor chillers using these systems are also provided.