The objective of this study was to evaluate the performance of the shrimp Litopenaeus vannamei and the tilapia Oreochromis niloticus in an integrated multitrophic aquaculture (IMTA) system combined with biofloc technology (BFT), under different bacterial dominance conditions: chemoautotrophic and heterotrophic. Two treatments were developed for this study (in triplicate): TQ (chemoautotrophic) and TH (heterotrophic). The TQ treatment was initiated 46 days prior to animal stocking, using inorganic fertilization with ammonium chloride and sodium nitrite salts. In the TH treatment, organic fertilization was applied after the animals were stocked, using sugarcane molasses when total ammonia nitrogen (TAN) reached 1 mg L⁻¹. A density of 400 shrimp m⁻² (0.98 ± 0.04 g) and 45 tilapia juveniles m⁻³ (25 ± 0.50 g) were used, maintained for 86 days in tanks with working volumes of 16 m³ and 4 m³, respectively. Continuous water recirculation occurred between tanks. Water quality parameters such as temperature, dissolved oxygen, and pH were monitored daily. Total ammonia, nitrite, nitrate, phosphate, total suspended solids, and settleable solids were monitored twice a week. Weekly biometric measurements of shrimp and biweekly measurements of fish were performed to assess growth performance. Based on the data collected, the following metrics were calculated: final average weight, weekly weight gain, feed conversion ratio, survival, biomass gain, and productivity. The results demonstrated that the prior fertilization in the chemoautotrophic treatment (TQ) prevented high concentrations of nitrogenous compounds for an extended period, due to the pre-establishment of bacteria in the system, compared to the heterotrophic treatment (TH). The increase in nitrogenous compounds in the TH treatment resulted in greater water use, reduced feed supply, and consequently lower shrimp growth performance compared to the chemoautotrophic system. Fish growth performance was not affected by the treatments. Therefore, the use of prior fertilization in the chemoautotrophic treatment (TQ) enabled higher final shrimp weight and productivity in the integrated system, in addition to greater environmental sustainability with zero water exchange.