The sulphur amino acids methionine (Met) and cysteine (Cys) and their derivative taurine (Tau) are metabolically active molecules with interlinked roles in nutritional requirements. Deficiencies in these nutrients are linked to poor growth and health; however, the impacts of these deficiencies on organ structure and function are largely unknown. This study examined the effects of dietary Met, Cys and Tau fed at different levels on yellowtail kingfish (YTK) liver histology and surface colour, plasma biochemistry and posterior intestine histology. Samples were collected from two dose–response feeding trials that quantified (1) the Tau requirement and sparing effect of Met by feeding YTK diets containing one of seven levels of Tau at one of two levels of Met and (2) the Met requirement and sparing effect of Cys by feeding YTK diets containing one of five levels of Met at one of two levels of Cys. YTK fed inadequate levels of dietary Met, Cys and Tau exhibited thicker bile ducts, less red livers, more intestinal acidic goblet cell mucus and supranuclear vacuoles and less posterior intestinal absorptive surface area. Further, thicker bile ducts correlated with less red livers (a*, R), whereas increased hepatic fat correlated with a liver yellowing (b*). Our results indicate a shift towards histological properties and functions indicative of improved intrahepatic biliary condition, posterior intestinal nutrient absorption and homoeostasis of YTK fed adequate amounts of Met, Cys and Tau. These findings may assist in formulating aquafeed for optimised gastrointestinal and liver functions and maintaining good health in YTK.