Biomarkers for monitoring shrimp health have been proposed but scarcely evaluated at the farm level. We analyzed several indicators of energy status in shrimp under farming conditions concerning stocking densities (100 m-2 with biofloc, 15 and 7 m-2). The influence of the year's season (temperature) was also analyzed, and, finally, an unfortunate event of White spot syndrome virus (WSSV) infection occurred on the 7 m-2 farms, adding another condition. At shrimp sampling from ponds, the effect of acute handling stress was also analyzed for indicators typically affected by such procedure with a 3- and 10-fold increase in glucose and lactate levels in hemolymph, respectively, regardless of density. This response was partially blunted at lower temperatures and WSSV incidence. Increased levels of protein in the hepatopancreas, adenylic energy charge (AEC) in both hepatopancreas and muscle and phosphagens in muscle were observed in shrimp from the 100 m-2 farms, suggesting a better nutritional and energetic status in shrimp cultured at high density with biofloc technology. Shrimp with WSSV presented lower hemocyanin levels in hemolymph, most likely associated with its role in the immune response. In WSSV-infected shrimp, the stress response regarding glucose increase was blunted, whereas a stress-induced increase in triglycerides (TG) levels in hemolymph was observed only with WSSV. Increased TG levels in those shrimp hepatopancreas could indicate a switch from carbohydrate to lipid-based metabolism associated with the preferential use of carbohydrates (Warburg effect) for virus replication in the early infection state.