Biofloc technology (BFT) is becoming popular in aquaculture. As the human population has rapidly increased, so has the demand for protein, driving the expansion of aquaculture. The increased use of aqua medicines in aquaculture has led to resistant microbes. BFT offers a promising, eco-friendly solution by promoting beneficial microbes to improve fish health and reduce chemical use, supporting the industry's long-term sustainability. BFT recycles waste without water exchange by maintaining an optimal carbon-nitrogen (C:N) ratio and adding an external carbon source, which promotes the growth of heterotrophic bacteria and other essential microbes that absorb ammonia from feed and waste, forming beneficial microbial aggregates. This study evaluated the effects of various C:N ratios in a jaggery-based BFT system on water quality, growth, feed efficiency, and the well-being of Heteropneustes fossilis. A completely randomized design with triplicates (2.33 kg/m³ in 1500 L tanks) was used to compare a control group without biofloc to three BFT treatments with C:N ratios of 8:1 (CN8), 12:1 (CN12), and 16:1 (CN16) over 180 days. Daily feeding was conducted at 5–2 % of the fish's body weight (initial weight of 5.0±0.5 g). Higher C:N ratios were linked to reduced dissolved oxygen, ammonia, and nitrite levels, alongside increased total suspended solids, floc volume, and heterotrophic bacteria counts, while the CN12 had the highest levels of beneficial microbes (Firmicutes and Actinobacteria), leading to superior fish growth, survival, and biomass compared to CN8 and CN16. The CN12 also showed better stress response, hematology, immunity, and antioxidant properties. Histologically, fish in CN12 and CN8 had healthier liver and intestines compared to CN16 and control. The results suggest that a C:N ratio of 12:1 was optimal for biofloc systems used in cultivating H. fossilis, enhancing both microbial growth and water quality.