A 112-day experiment was conducted to investigate the influence of the content of microbial protein and poly-β-hydroxybutyrate (PHB) in biofloc on the growth, productive performance, and hemato-biochemical parameters of Nile tilapia (Oreochromis niloticus) fingerlings. The fish cultivated using the biofloc technology system (BFT) were reared at two stocking densities (40 and 80 fish m−3) and fed with a gradual protein-restriction diet (LPBFT). Two clear-water controls (CW) were used for the estimation of the density: High protein control (HP) and Low protein control (LP). The fish from HP (HPCW) were fed with commercial pellets containing 45% crude protein (CP) during the initial seven weeks and 35% CP during the final nine weeks. The fish from LP (LPCW) and LPBFT were fed with 35% CP during the initial seven weeks and 25% CP until harvest. The BFT microbial proteins were observed to compensate for the restriction of the dietary proteins. A 22.2% net reduction in the CP given to fish of 4.29 ± 0.25 g to 40.5 ± 5.4 g BW, and by 28.6% to fish of 40.5 ± 5.4 g to 182.6 ± 5.2 g BW did not negatively affect the survival, growth, and health of the fingerlings. Weight gain was significantly higher in LPBFT than LPCW at both stocking densities, and no significant differences were observed between the fish raised in CW and those fed on a high protein diet. The net yield of LPBFTs was increased by 27.9–29.5% compared to LP controls, while FCR was improved by 1.6% with the incorporation of BFT. When the concentration of heterotrophic bacteria (HB) reached 5.06 × 105 and 5.66 × 105 CFU mL−1, the maximum value of microbial proteins was 33.0 ± 5.9% for LPBFT-L and 32.5 ± 6.2% for LPBFT-H, respectively. The variables associated with the cumulative variance in the percentage of microbial protein were the concentration of HB (84.3%), followed by total organic carbon (8.6%) and NO3-N (4.6%). The PHB increased significantly with an increase in the concentration of HB (R = 80%) and showed a 75% correlation with the microbial protein content. During the final week of the culture, 1 mL of floc containing an average of 5.22 ± 1.78 × 105 CFU mL−1 produced 18.57 ± 2.22 nmol 100 g−1 DW of PBH. The blood biochemistry profile from LPBFT was similar to the high protein controls. Our data confirm the potential of the application of BFT during the early stages of tilapia growth, without affecting the survival, productive parameters, or the overall health of the organisms.