For many fish species, environmental colour may act either as a source of stress or as a stress-buffer, alleviating behavioural and physiological responses after a stressful situation. While much is known on the effects of environmental colour on fish stress parameters, knowledge on the effects of stress on fish colour preferences is still lacking. In order to test the effects of stress on colour preference in fish, in this work, we exposed rainbow trout embryos (Oncorhynchus mykiss) to stressful conditions (air exposure, pheromone alarm cue or control, with minimal stress) from 19 to 44 days post fertilization (dpf). They were then raised up to 56 dpf in bright, dark, green or blue environments. After that, fry were individually tested for colour preference in a three-chambered arena where they could choose between green and blue areas. The time spent in the blue and in the green chamber was compared between experimental groups. Rainbow trout fry exposed to minimal stress (control) or to biotic stress (pheromone alarm) showed increased time in the blue environment, with little effect of ambient colour where they were raised. However, fish that experienced air exposure stress showed a lack of colour preference irrespective of the colour they were raised in afterwards. These results imply that early life stress affects colour preference in rainbow trout, suggesting that abiotic stressors, such as air exposure, may affect colour perception or behavioural plasticity in young fish. If the results presented herein are corroborated by future studies in fish at different life stages, beyond the embryonic phase, colour preference tests may be used as an additional and potential welfare indicator to estimate, in a retrospective manner, which stressors were faced by the individuals during early stages. By knowing whether or not their fish were exposed to certain stressful conditions may allow farmers to better adapt fish rearing conditions and to implement strategies that alleviate any long-term impacts that may exist, and, therefore, improve fish welfare.