Land use change is accelerating globally at the expense of biodiversity and ecosystem functioning. Invertebrates are numerically dominant and functionally important in old growth tropical rain forests but highly susceptible to the adverse effects of forest degradation and fragmentation. Ants (Formicidae) and termites (Blattodea: Termitoidae) perform crucial ecosystem services. Here, the potential effects of anthropogenic disturbance on ant and termite communities in dead wood are investigated. Community composition, generic richness, and occupancy rates of ants and termites were compared among two old growth sites (Danum Valley and Maliau Basin) and one twice-logged site (the Stability of Altered Forest Ecosystems’ (SAFE) Project), in Sabah, Malaysian Borneo. Occupancy was measured as the number of ant or termite encounters (1) per deadwood items, and (2) per deadwood volume, and acts as surrogates for relative abundance (or generic richness). Termites had a lower wood-occupancy per volume in logged forest. In contrast, there were more ant encounters, and more ant genera, in logged sites and there was a community shift (especially, there were more Crematogaster encounters). The disruption of soil and canopy structure in logged forest may reduce both termite and fungal decay rates, inducing increased deadwood residence times and therefore favoring ants that nest in dead wood. There is an anthropogenic-induced shift of dead wood in ants and termites in response to disturbance in tropical rain forests and the nature of that shift is taxon-specific.