This contribution deals with the development of suitable operating strategies for diesel/kerosene-fueled fuel cell APUs. The focus is on the autothermal reformer (ATR) and the water-gas shift (WGS) reactor. In the first part shutdown experiments under high-temperature shift (HTS) conditions were used to identify the possible detrimental effect of higher hydrocarbons on the activity and stability of two commercial WGS catalysts. The results indicated that 220 ppmv higher hydrocarbons had no negative effect on the catalyst activity/stability. The second part presents fuel processing system experiments, which revealed much higher concentrations of higher hydrocarbons during transients like startup/shutdown than the concentrations investigated in the first part. Through the development of new startup/shutdown strategies concentrations of higher hydrocarbons were lowered by a factor of up to 10 for startup and of up to 400 for shutdown. The results were reproduced using four different diesel and kerosene fuels. The newly developed strategies improve fuel conversion in the reformer and may possibly prevent catalyst deactivation in the water-gas shift reactor during transient conditions. (C) 2015 Elsevier Ltd. All rights reserved.