The external coloration of fish is a key driver in consumer buying decisions and is typically altered during sexual maturation in salmonids. Farmed Atlantic salmon ( Salmo salar L.) exhibiting distinct phenotypes from the typical silver and nuptial coloration were described in terms of sexual development, flesh quality, and skin pigment profiles. Reconditioning of skin coloration during storage was also tested (CIE[1976]L*a*b*) with the overall view to optimize quality management. The intermediary phenotype never reflected significant deteriorations of flesh quality. It originated from a lack of purine pigments (guanine and hypoxanthine), revealing the carotenoid compounds dominated by the yellow-orange beta-carotene. The resulting distinctive lightness and yellowness were reduced by direct ice contact at a post-mortem stage. Storage conditions can be optimized to improve and standardize the coloration of whole-fish, yielding superior flesh quality parameters. This would facilitate product quality grading during primary processing and also increase product acceptance and attractiveness.