The Biofloc Technology System (BFT) is characterized by stimulating the development of a microbial community that acts mainly in the maintenance of water quality but also promotes other benefits such as increased productivity, biosafety and serves as a supplementary source of food for reared animals. Two main groups of bacteria are involved in nitrogen removal in this system: heterotrophic bacteria and autotrophic nitrifying bacteria, present in the aggregates. Different fertilization techniques can be used for the formation and maintenance of bioflocs, depending on which group of bacteria the predominance is preferred. This study aimed to analyze the effect of different organic fertilization techniques on the bioflocs establishment, amount of water used, the production of suspended solids and the growth performance of Litopenaeus vannamei reared in the BFT System. Shrimp juveniles were stocked in 150-liter tanks at a stocking density of 300 shrimps/m³. Three treatments (in triplicate) were tested using different fertilization techniques: 1) without supplementary organic fertilization; 2) organic fertilization according to nominal ammonia reading (heterotrophic/chemoautotrophic = “mixed” system) and 3) organic fertilization according to estimated ammonia production (heterotrophic). The temperature, salinity, dissolved oxygen, pH, ammonia, nitrite, nitrate, alkalinity and total suspended solids (TSS) of the water were monitored. The water quality parameters were influenced by the treatments with differences found in the concentrations of ammonia, nitrite, nitrate, pH, alkalinity and TSS. Ammonia levels were higher in control treatment since no organic fertilization was performed. Nitrite levels were lower in heterotrophic system since the nitrifying pathway was suppressed due to daily fertilization, also resulting in lower nitrate levels. There were significant differences in the growth performance parameters, with the highest final weight and yield, as well as the lowest FCR, found in the mixed treatment. There were no significant differences among survival. The mixed system treatment used less water during production cycle compared to other treatments while the volume of solids removed was almost four times greater in the heterotrophic treatment compared to the others. These results show that adopting a mixed heterotrophic/chemoautotrophic biofloc system improves shrimp growth performance, optimize water use and decrease solids production.