Background Rice can accumulate arsenic (As) to relatively high concentrations due to the general flooding practices in rice cultivation, and organic matter in the soil strongly affected As bioavailability to rice plants. The influence of organic matter input on the As transformation in paddy soil and As uptake into rice plants is an area that is rarely investigated. Methods Biogas slurry (BGS), a commonly used organic fertilizer, was applied to an As contaminated paddy soil, in order to investigate the influence of organic matter on As transformation in the paddy soil and As accumulation in rice plants.Results Application of BGS significantly increased the As accumulation in rice plants, especially for methylated As species. Results showed that the concentrations of dissolved organic carbon (DOC) and dissolved Fe(II) in the soil solution were significantly increased by the BGS addition into the paddy soil, and were significantly correlated to the As concentration in the soil solution (P<0.01). The increase of soil pH and the decrease of the soil redox potential (Eh) were observed as well. These alteration of soil characteristics elevated the As release from soil particles to the soil solution under the addition of BGS. The increased concentrations of dimethylarsinic acid (DMAs(V)) and monomethylarsonic acid (MMAs(V)) in the soil solution, and the volatilized As of trimethylarsine (TMAs) from the paddy soil, suggested that As methylation and volatilization in the soil were also enhanced by BGS addition. The concentrations of methylated As species in rice husks and grains were increased by 105.8-105.9 % and 99.7-112.2 %, respectively. Conclusion These results suggested that the use of organic fertilizer, such as BGS in As-contaminated paddy soil, can significantly alter the behavior of As in soil-rice system and enhance As accumulation in rice plants and should therefore be avoided.