In super-intensive shrimp culture, water supplements are often used to adjust and stabilize water quality parameters, microbiological and environmental conditions, as well as suppress undesirable microorganisms. In addition, some water supplements are frequently utilized to boost the diatom population in water. These microorganisms are well known to enhance the shrimp growth performance, and present inhibitory effect against pathogenic vibrio. The present study evaluated the effect of sodium metasilicate (SM) supplementation in the culture water on the diatom population, water quality, zootechnical performance and economics of indoor commercial-scale biofloc-based culture. Litopenaeus vannamei (PL10, 4.1 ± 1.5 mg initial weight) were stocked in eight 500 m−2 commercial ponds with (BFT-SM) and without SM supplementation (BFT as a control), with four replicates per treatment. After 92 days (single phase, direct stock), the average values of silica (SiO2) were 8.2 mg L−1 in BFT-SM and 2.5 mg L−1 in BFT (control) (P < 0.05). Microscopical analysis indicated higher diatom dominance in BFT-SM, corroborated by higher chlorophyll-A concentrations. The shrimp biomass and yield were significantly higher in BFT-SM with 3.0 kg m−3 and 36.2 ton ha cycle−1 compared to BFT with 2.8 kg m−3 and 33.5 ton ha cycle−1, respectively. The BFT-SM treatment produced a 9.75% higher net profit margin than the BFT treatment and a 10.55% increase in revenue. Our study demonstrated positive impacts of SM supplementation on diatom population, resulting in enhanced shrimp performance and economic returns in indoor commercial-scale biofloc-based L. vannamei culture.