Most animals experience temperature variations as they move through the environment. For ectotherms in particular, temperature has a strong influence on habitat choice. While well-studied at the species level, less is known about factors affecting the preferred temperature of individuals. Especially lacking is information on how physiological traits are linked to thermal preference and whether such relationships are affected by factors such feeding history and growth trajectory. This study examined these issues in the common minnow Phoxinus phoxinus, to determine the extent to which feeding history, standard metabolic rate (SMR) and aerobic scope (AS), interact to affect temperature preference. Individuals were either: 1) food-deprived for 21 days, then fed ad libitum for the next 74 days; or 2) fed ad libitum throughout the entire period. All animals were then allowed to select preferred temperatures using a shuttle-box, and then measured for SMR and AS at 10°C, estimated by rates of oxygen uptake. Activity within the shuttle-box under a constant temperature regime was also measured. In both food-deprived and control fish, SMR was negatively correlated with preferred temperature. The SMR of the food-deprived fish was elevated compared to the controls, probably due to the effects of compensatory growth, and so these growth-compensated fish preferred temperatures that were on average 2.85°C cooler than controls fed a maintenance ration throughout the study. Fish experiencing compensatory growth also displayed a large reduction in activity. In growth-compensated fish and controls, activity measured at 10°C was positively correlated with preferred temperature. Individual fish prefer temperatures that vary predictably with SMR and activity level, which are both plastic in response to feeding history and growth trajectories. Cooler temperatures probably allow individuals to reduce maintenance costs and divert more energy towards growth. A reduction in SMR at cooler temperatures, coupled with a decrease in spontaneous activity, would also allow individuals to increase surplus aerobic scope for coping with environmental stressors. In warming climates, however, aquatic ectotherms could experience frequent fluctuations in food supply with long-lasting effects on metabolic rate due to compensatory growth, while simultaneously having limited access to preferred cooler habitats.