<p>The nursery phase in autumn is an important strategy for scaling up tilapia farming in subtropical regions, which otherwise suffers from a lack of fingerlings in winter. Tilapia nursery is carried out in a semi-intensive system in ponds; however, the biofloc technology system (BFT) has productive, environmental, and health advantages. This study aimed to compare the production of Nile tilapia (<i>Oreochromis niloticus</i>) juveniles in two rearing systems during autumn through the evaluation of fish growth performance, environmental, and hematological parameters, as well as production costs. The 46-day experiment was conducted on a pilot scale, with four experimental units per system stocked with fingerlings averaging 1.95 ± 0.32&#xa0;g. In the semi-intensive system, 25 m³ ponds were used, and each was stocked with 1100 fingerlings (44 fish m⁻³). In the super-intensive system, 4 m³ circular tanks were used, each stocked with 2200 fingerlings (550 fish m⁻³). The production of tilapia juveniles in BFT showed greater stability of water quality parameters throughout rearing in association with higher water temperature owing to the greenhouse. This allowed similar growth between fish in both systems, but with productivity 12.7-fold higher in BFT, while consuming 29.6 times less water. Hematological parameters among fish in the two systems were also similar. Moreover, the BFT system demonstrated a 6.2% reduction in total operating costs compared to the semi-intensive pond system, positioning it as a more cost-effective option for producing Nile tilapia juveniles in subtropical regions. These results highlight the BFT system’s potential as a viable alternative for rural fish farmers.</p> Graphical Abstract <p></p>