Abstract Three types of biogranules treating wastewater containing various sulphate concentrations were examined using scanning and transmission electron microscopies. The two biogranules treating wastewater containing sulphate up to 2000 mg·l −1 showed high degrees of activities. However, activities of the third biogranules, which contained 102 mg-S·(g-VSS) −1 after treating wastewater containing sulphate up to 7500 mg·l −1 for over 286 days, dropped drastically. Microscopic examinations showed that precipitates accumulated in the biogranules treating sulphate-bearing wastewater; the degrees of precipitation increased with sulphate concentration in wastewater and the duration of treatment. Excessive precipitation was found throughout the entire biogranule cross-section of the third biogranules. Analyses by X-ray spectrometry further showed that the precipitates were mainly composed of sulphur, plus copper, iron and nickel presumably in the form of metal sulphides. These observations suggest that the inhibition of bioactivities of anaerobic granules was likely resulted from the accumulated sulphureous precipitates on the bacterial surface. This point was overlooked by previous investigators who tended to attribute the inhibition to the toxic effects of either sulphate, sulphide or un-dissociated H 2S.