The present invention provides automated systems and methods for monitoring column performance in process chromatography, and applications thereof. In an embodiment, column performance is monitored by generating a plurality of process values such as, for example, conductivity values or pH values with a detector during a chromatography step transition between a first mobile phase liquid and a second mobile phase liquid. The process values are transformed to form transformed process values in which noise present in the process values is suppressed. Column performance parameters are calculated based on the transformed process values and displayed during movement of the second mobile phase liquid through the chromatography column. The displayed performance parameters enable an operator to make a determination, for example, regarding the quality of the chromatography column packing and whether to continue the chromatography process or stop the chromatography process until the chromatography column can be repacked or replaced.