Release of nanoceria (nCeO2) into the environment has caused much concern about its potential toxicity, which still remains poorly understood for soil microorganisms. In this study, nanoceria and cerium (III) nitrate at different doses (10, 100 and 500 mg/kg) were applied to bok choy (Brassica rapa subsp. chinensis), grown in potting soil, to investigate the responses of soil bacterial communities to nanoceria (NC) and ionic cerium (IC) applications. The results showed that bacterial richness was slightly increased in all cerium treatments relative to the negative control without cerium amendment (CK), but a significant increase was only found in IC500. The patterns of bacterial community composition, predicted functions and phenotypes of all NC treatments were significantly differentiated from IC and CK treatments, which was correlated with the contents of cerium, available potassium and phosphorus in soil. The co-occurrence network of bacterial taxa was more complex after exposure to ionic cerium than to nanoceria. The keystone taxa of the two networks were entirely different. Predicted functions analysis found that anaerobic and Gram-negative bacteria were enriched under nanoceria exposure. Our study implies that Proteobacteria and nitrifying bacteria were significantly enriched after exposure to nanoceria and could be potential biomarkers of soil environmental perturbation from nanoceria exposure.