Biofloc Technology (BFT) represents an alternative aquaculture system that is able to enhance production efficiency and intensify P. mesopotamicus (pacu) production. This pioneering study explores the molecular mechanisms underpinning pacu responses to bioflocs. Juveniles (n = 90; 68.86 +/- 4.43 g) were randomly assigned to either BFT or a Recirculating Aquaculture System (RAS), with nine replicates (300-L water boxes) per system. Biometric assessments were conducted at the onset and conclusion of the 45-day experimental period, with final-day collections of skeletal muscle, liver, kidney, and spleen samples. Total ammoniacal nitrogen levels were similar (p > 0.05) between BFT (0.14 mg/L) and RAS (0.25 mg/L), while nitrite levels were significantly lower (p = 0.024) in BFT (0.27 mg/L) compared to RAS (0.64 mg/L), and nitrate levels were higher (p = 0.001) in BFT (45.83 mg/L) than in RAS (29.17 mg/L). The juveniles demonstrated superior productive performance in BFT (p < 0.05), as evidenced by enhanced weight gain, growth, and feed conversion. Among the genes, there were no significant differences in hepatic or muscle igf-1 expression levels between BFT and RAS (p > 0.05). However, il-1 beta mRNA was more highly expressed in the kidneys of juveniles in BFT (p = 0.013), suggesting that microorganisms present in bioflocs may contribute to improved immune resistance by stimulating the innate immune response. Therefore, BFT represents a sustainable and valuable system for rearing pacu, as it enhances growth performance, ensures better water quality, improves productive efficiency, and bolsters the innate immune response in juveniles.