Although sustainable forestry methods such as Reduced Impact Logging (RIL) have lower impacts on biodiversity compared to conventional logging, the direct and indirect effects of RIL are poorly understood. Additionally, studies focusing on specific habitats may fail to detect cross-habitat impact variation or the effect on taxa which utilize multiple habitats, i.e. amphibians. We therefore investigated the responses of amphibians in stream and terrestrial habitats to RIL and its direct/indirect impacts. We analysed data from anuran communities sampled before and after RIL within the Deramakot forest reserve in Sabah, Malaysian Borneo. Using multi-species community occupancy models, we determined species and community responses to RIL and covariates representing the direct (leaf depth and canopy closure) and indirect (distance to logging roads and skid trails) effects of logging. Diversity profiles and dissimilarity indices derived from occupancy model results were used to identify shifts in diversity/evenness and community dissimilarity respectively following RIL. Indirect logging impacts (distance to logging roads/skid trails), proved a better predictor of amphibian occupancy in stream habitats compared to direct logging impacts (leaf litter depth shifts), with the opposite trend observed in terrestrial habitats. Anurans in stream and terrestrial sites exhibited greater dissimilarity and community occupancy after logging compared to control sites, with all diversity metrics (species richness, Shannon and Simpson diversity) increasing in logged stream sites. These findings, contrary to our expectations, suggest that whilst amphibian species in different habitats exhibit variable responses to direct and indirect RIL impacts, they exhibit similar community level responses to RIL across habitats.