The prevalence of black spot shell disease is increasing among marine crustaceans worldwide. Rising seawater temperatures – often stressful for ectothermic species – are assumed to enhance the occurrence of shell disease. In the North Sea > 50% of local populations of the brown shrimp (Crangon crangon) are affected by the disease. While fisheries are suffering because diseased crustaceans are barely merchantable, the impact of shell disease on life history traits of crustaceans is little understood. To determine the role of temperature on the development of black spots and its implications for survival and physiology in the brown shrimp, a prolonged (3 months) thermal stress experiment was performed. We measured the increment of shell disease and the effect of molting in shrimps kept at control (15 °C = equivalent to the seafloor temperature in the North Sea during sampling) and increased temperature (20 °C = according to predictions for the end of the century). The resting metabolic rate was analyzed to determine the physiological state of diseased compared to non-diseased animals. In the present study, the warmer temperature in the range of 20 °C did not increase the spot size of shell disease and no differences were observed between the two temperatures. The process of molting thereby seemed to diminish and in most of the cases even completely remove the signs of shell disease. At 15 °C but not at 20 °C, metabolic rate was reduced in diseased in contrast to healthy individuals. This study showed that shell disease might lead to a higher mortality rate and an impairment of the physiological state in C. crangon.