The plant Strobilanthes cusia contains various antibacterial components, but the mechanisms behind its antimicrobial activity are not yet fully understood. This study demonstrates that alterations in components due to different pretreatments significantly impacted the antimicrobial activity of S. cusia biomass. Biomass dried using microwave pretreatment, which contained a high amount of indican, exhibited the lowest antibacterial activity, whereas heat-dried biomass without indican showed the highest antibacterial activity. High-performance liquid chromatography analysis indicated that pretreatments influenced the ratios of indican, indoxyl, indigo, and indirubin in S. cusia biomass, likely due to the effect of pretreatments on β-glucosidase activity. Extracts with higher levels of indoxyl, an intermediate product of indican hydrolysis, exhibited stronger inhibitory effects against Staphylococcus aureus. Indoxyl increased the NAD+/NADH ratio, which led to elevated hydrogen peroxide generation and subsequent cell damage. Furthermore, transmission electron microscopy, scanning electron microscopy, and confocal laser scanning microscopy revealed distinct morphological changes in cells exposed to indoxyl. Finally, leveraging the water-soluble properties of indoxyl, we propose a novel approach using microwave drying assisted by β-glucosidase to enhance the antimicrobial activity of S. cusia biomass. These findings provide a theoretical and methodological foundation for the evaluation and future application of S. cusia's bioactive substances.