The coexistence and distribution of nitrate and vanadate co-pollutants in groundwater have become an environmental problem, which needs to be urgently addressed. Although recent advances in the combination of activated sludge and agro-industrial waste have improved co-pollution removal, conventional activated sludge methods focused primarily on enhancing abiotic priming effects, neglecting the biological priming effects of colonizing microorganisms in agro-industrial waste, which limited the insights into the treatment mechanism. The removal of nitrate and vanadate was microbially mediated and highlighted the abiotic enhancement mechanism of the solid phase carbon source in the presence of microorganisms. Microorganisms in conventional activated sludge methods should be continuously incubated with the co-contaminants for at least 30 days to demonstrate stable and effective removal of the co-contaminants. This study demonstrated that the coupled system of unsterilized agro-industrial waste and untamed sludge achieved competitive nitrate (0.1319 h−1) and vanadate reduction rates (0.0359 h−1) without sludge acclimation. Compared with the control experiments, the nitrate and vanadate reduction rate increased 1.95–7.62 times and 2.85–5.36 times, respectively. The colonized functional microbes carried by agro-industrial waste played an important role in the microbial priming effect of co-pollutant removal. This work contributes to the efficient and economical treatment of the co-pollution of inorganic salts and heavy metals. Display omitted •Indigenous microbes attached to natural biomass had the ability to degrade nitrate or V(V).•Interspecies cooperation among microbes eliminated the sludge cultivation period.•The key metabolic pathways related to energy metabolism were significantly upregulated in the coupled system.•Priming effects of indigenous microbes of natural biomass played an essential role.