This study evaluated the effect of inoculating a commercial Bacillus spp. mixture (Bacillus subtilis and Bacillus licheniformis) into a closed-loop aquaponics system integrating Nile tilapia (Oreochromis niloticus) and hydroponic lettuce (Lactuca sativa). Inoculation occurred twice weekly at 0.02 g L⁻¹ into the biofilter component, comparing treated systems against an untreated control. Nutrient dynamics, plant performance, phosphorus budgets, and microbial counts were assessed. Inoculation significantly influenced nutrient dynamics (p < 0.05). Bacillus-treated systems exhibited a faster decrease in total ammonia nitrogen, with levels nearly exhausted by week 3, accompanied by a faster spike in nitrite and nitrate compared to the control. Dissolved orthophosphate concentrations significantly increased in treated systems (p < 0.001) after week 3, leading to substantially enhanced lettuce growth. Lettuce dry mass in Bacillus-treated systems reached 4.09 ± 0.87 g compared to 1.30 ± 0.92 g in controls (p = 0.019), with higher tissue phosphorus content (0.54% vs 0.25%, p = 0.0001) and elevated chlorophyll index (7.27 vs 5.27, p < 0.0001). Viable plate counts showed 6.0 × 10⁵ CFU mL⁻¹ in treated water versus zero detectable growth in controls. Overall, Bacillus application effectively accelerated nitrification and promoted plant growth in aquaponics.