• A basic dye in industrial effluent poses significant environmental threats due to their toxicity. • Nano-lignin was synthesized from the leftover rice straw collected from the paddy field. • The synthesized nano lignins were characterized with the help of SEM, DLS and FTIR. • The synthesized nano lignins effectively adsorbed the toxic dyes from the water bodies. In the present study, nano-ligninwas synthesized from rice straw using Lactobacillus rhamnosus for the cost-effective removal of harmful dye from wastewater. The UV absorption maxima of the synthesized nano-lignin were around 280–290 nm. Several FTIR bands between 1075 cm −1 to 3500 cm −1 confirmed the successful confirmation of nano-lignin synthesis from rice straw. STEM and DLS studies confirmed the spherical morphology of nano-lignin with an average particle size of 286.3 nm. The nano-lignin showed a negative zeta potential value of −16.9 ± 5.94 mv. Afterward, nano-lignin was used to remove basic methylene blue (MB), phenol red (PR),and brilliant green (BG) dye from aqueous solutions. The adsorption of these dyes increased with increased incubation time. The adsorption concentration of the MB, PR, and BG dyes ranged from 3.5 mg/g to a final of 24 mg/g, 2.5 mg/g to 42.5 mg/g, and 1.5 gm/g to 5.5 mg/g, respectively.