To evaluate effect of substrate integration in biofloc based system, a 52‐day growth experiment was conducted using black tiger shrimp, Penaeus monodon juveniles (3.32 ± 0.07 g). The factorial design consisted of floc, F (with or without) as first factor and substrate (bamboo mat, B; nylon mesh, N; and without substrate) as second factor. This resulted six treatments; F + B, F + N, F, B, N and a control without biofloc and substrate. Shrimps were stocked at 110 nos. m–3 in Fibre Reinforced Plastic (FRP) tanks and, rice flour was used as carbon source in biofloc based treatments. Incorporation of nylon mesh and bamboo mat in biofloc system trapped 31.3%–38.6% and 8.5%–13.5% total suspended solids respectively and reduced bottom solid deposition. Among the substrate based groups, significantly better development of biofilm with higher microbial population noticed in F + B compared with nylon mesh. Similarly, significantly higher final growth (p < 0.01) was recorded in F + B system followed by F + N while no significant difference in body weight recorded among floc, F or substrate based groups (B, N). Biofloc and substrate integration (F + B and F + N) resulted significantly (p < 0.01) lower feed conversion ratio compared to control and floc. Incoporation of bamboo substrate in biofloc, (F + B) improved shrimp immune responses through higher hemocyte counts and prophenoloxidase activity compared to other treatments. The study revealed that integration of substrate in the biofloc system improved growth performance, FCR and immune parameters in shrimp by trapping the suspended biofloc particles, better water quality parameters, enhanced biofilm growth and provision of quality natural food.