Carboxylated multiwalled carbon nanotubes (MWCNTs-COOH) have become a growing concern in terms of their fate and toxicity in aqueous environments. Methane (CH4) is a major product of organic matter degradation in waterlogged environments. In this study, we determined the effect of MWCNTs-COOH on the production of CH4 from propionate oxidation in paddy soil enrichments. The results showed that the methanogenesis from propionate degradation was accelerated in the presence of MWCNTs-COOH. In addition, the rates of CH4 production and propionate degradation increased with increasing concentrations of MWCNTs-COOH. Scanning electron microscopy (SEM) observations showed that the cells were intact and maintained their structure in the presence of MWCNTs-COOH. In addition, SEM and fluorescence in situ hybridization (FISH) images revealed that the cells were in direct contact with the MWCNTs and formed cell-MWCNTs aggregates that contained both bacteria and archaea. On the other hand, nontoxic magnetite nanoparticles (Fe3O4) had similar effects on the CH4 production and cell integrity as the MWCNTs-COOH. Compared with no nanomaterial addition, the relative abundances of Geobacter and Methanosarcina species increased in the presence of MWCNTs-COOH. This study suggests that MWCNTs-COOH exerted positive rather than cytotoxic effects on the syntrophic oxidation of propionate in paddy soil enrichments and affected the bacterial and archaeal community structure at the test concentrations. These findings provide novel insight into the consequences of nanomaterial release into anoxic natural environments.