Separate testing protocols for fuel cell startup (SU) and shutdown (SD) are developed to distinguish between the effects of \SU\ and \SD\ on performance degradation. The internal currents during \SU\ and \SD\ operation are measured in a segmented cell to evaluate the charge exchanged between the active (H2/Air) and passive (Air/Air) portions of the cell. Cells with different membrane-electrode assemblies (MEAs) are subjected to \SU\ or \SD\ sequences to evaluate the time evolution of spatially resolved decrease of performance and electrochemical active surface area (ECSA). We examine the influence of the cathode and anode Pt loading, and the type of carbon for cathode catalyst support. Both the \CO2\ emissions and the charges exchanged increase with the common residence time of air and hydrogen in the anode compartment. However, the evolved \CO2\ accounts for less than 25% of the total exchanged charge. Startups are consistently more damaging than the shutdowns, evidenced by more evolved \CO2\ and charge exchanged, severe \ECSA\ decrease, and higher performance losses.