Calcium carbonate often precipitates in anaerobic reactors treating wastewater with high calcium content. The aim of this paper is to study the effect of wastewater composition on calcium carbonate precipitation in upflow anaerobic sludge blanket (UASB) reactors. Two laboratory-scale UASB reactors were operated with calcium-containing influents using acetate and carbohydrate as substrate, respectively. There was an obvious accumulation of inorganic precipitate observed in the biogranules. Observations via scanning electron microscope (SEM) and energy dispersive spectroscopy (EDS) showed that the acclimated biogranules in the two reactors differed in microstructure. Calcium carbonate was found to have precipitated on the surface of acetate-degrading biogranules, but precipitated at the core of the carbohydrate-degrading biogranules. The results indicated that substrates had significant influence on the location of calcium carbonate precipitation in anaerobic granular sludge, which was expected due to the different methanogens distribution and pH gradient within the granular sludge degrading various substrates. Moreover, the location of calcium carbonate precipitation substantially affected the specific methanogenic activity (SMA) of the granular sludge. The SMA of the acetate-degrading biogranules dropped from 1.96 gCOD·gVSS·d to 0.61 gCOD·gVSS·d after 180-d of operation in the reactor. However, the SMA of the carbohydrate-degrading biogranules was not adversely affected by calcium carbonate precipitation.