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Durability of proton exchange membrane fuel cell systems under cold weather conditions is essential and a critical challenge for transportation applications. During cold storage the water remaining in the cells can freeze causing damage to the cell components. In order to avoid this degradation, fuel cells are commonly purged with dried gases during shutdown prior to its storage at subzero temperatures. This work investigates cold storage of PEMFC systems at temperatures down to -40°C with the aim of developing a shutdown procedure that leads to minimal degradation due to cold storage, while meets energy efficient and time requirements of aeronautical applications. To that end, several experiments were carried out with two different stacks (a 4 kW liquid cooled and a 100 W air cooled) under a wide range of operating parameters: cathode gas, purge temperature, anode and cathode gas purge flow rates, purge time and cold storage temperature. The fuel cell performance degradation due to ice formation was measured by the polarization curves conducted prior and after every F/T cycle. The effects of these operating parameters on the durability of the PEMFC systems under cold storage are evaluated. The obtained experimental results showed that very long purge process lead to further performance degradation at -10°C than shorter process at -40°C, which indicates that eliminating all remained water in the cells is not only inefficient, but also lead to degradation due to the drying process. Moreover, guidelines to improve shutdown procedure for cold storage of proton exchange membrane fuel cell systems for aeronautical applications are discussed.