Selective logging has been widely employed as a management practice in tropical forests due to its reduced impact on biodiversity. However, by altering microclimatic conditions, logging could affect soil fauna responsible for nutrient cycling and the long-term dynamic of the forest. We investigated how selective logging affected termite species richness, composition, and the distribution of species in trophic groups, as well as the natural response of termites to gradients of soil conditions. Termites and edaphic variables were sampled in 32 permanent plots in southern Amazonia. Plots were subject to selective logging for 10–31 years before termite sampling. Time post-management was associated with changes in termite species composition, and wood-feeding termites were more abundant in recently logged areas. Nevertheless, most of the variation in termite species richness and composition can be attributed to the natural variation in soil clay content. Moreover, soil-dweller species, a vulnerable group strongly linked to soil decomposition, were present in all plots. These results suggest that the impact of selective logging on termite communities might be milder compared with other types of disturbance. It is likely that the decomposition process performed by termites, and consequently long-term ecosystem functioning, is preserved under selective logging.