Manganese (Mn) in acidic paddy soil has large potential in emigrating from the soil and pollute adjacent ecosystems. Single microorganisms modulate the biogeochemistry process of Mn via redox reactions, while the roles of microbial aggregates (e.g. periphytic biofilm) in modulating its biogeochemical cycle is poorly constrained. Here we collected a series of periphytic biofilms from acidic paddy fields in China to explore how periphytic biofilm regulates Mn behavior in paddy fields. We found that periphytic biofilms have large Mn accumulation potential: Mn contents in periphytic biofilm ranged from 176 ± 38 to 797 ± 271 mg/kg, which were 1.2-4.5 folds higher than that in the corresponding soils. Field experiments verified the Mn accumulation potential, underlining the biofilms function as natural barriers to intercept Mn emigrating from soil. Extracellular polymeric substances, especially the protein component, mediated adsorption was the main mechanism behind Mn accumulation by periphytic biofilm. Microorganisms in periphytic biofilms in general appeared to have inhibitory effects on Mn accumulation. Climatic conditions and nutrients in floodwater and soil affect the microorganisms, thus indirectly affecting Mn accumulation in periphytic biofilms. This study provides quantitative information on the extent to which microbial aggregates modulate the biogeochemistry of Mn in paddy fields.