This study aimed to evaluate the yields of by-products and residues and the morphometry of juvenile tambaqui Colossoma macropomum undernutrition with different levels of lysine. Diets were elaborated containing 6.60, 9.72, 12.84, 15.96, 19.08, and 22.20 g kg-1 of total lysine, and these were fed to fish distributed in 18 tanks (310 L each one) for 90 days. Morphometric analysis, measurements of whole fish, by-products, and residues were taken and compared to each other. All variables were validated using ANOVA, Tukey's test, and quadratic regression analysis (P < 0.05). No differences were found for the morphometric variables (P > 0.05). The ratio between morphometric data for the standard and total length showed significance at levels of 9.72 and 15.96 g kg-1 (P = 0.03). The gutted fish and fillets, the protein and lipid contents of the fillets, and the weights and lengths of the intestines did not change (P > 0.05). Moisture was modified with lysine at levels of 22.20 g kg-1 (P = 0.00), and minerals, between 6.60 and 22.20 g kg-1 (P = 0.01). The increase in lysine levels in the diet led to an increase in fin weight (P = 0.00). It was concluded that the addition of lysine in the diet did not directly influence the morphometry and yields of the fish in the juvenile phase, but it did affect the fin waste and the skin by-product.