Borneo is one of the most biodiverse regions on the planet but half of Borneo’s forest has been logged and millions of hectares replaced by oil palm plantation. Decomposing biodiversity into its underlying component parts may reveal mechanisms by which diversity loss might be mitigated. I sampled beetles (order: Coleoptera) at the Stability of Altered Forest Ecosystems Project in Sabah to quantify shifts in biodiversity associated with logging and clearing of tropical lowland forest for oil palm plantation. While logged forest maintained high species richness, the beetle species which persisted there were of lower conservation value. Beta-diversity mitigated losses in alpha-diversity in heavily-logged forest to some extent, and in multiple beetle taxa beta-diversity was greatest in that habitat. In both logged and unlogged forest, high beta-diversity was maintained through balanced variation in community composition. Oil palm plantations supported very few beetle species and although beta-diversity remained high, that beta-diversity was attributed to fluxes in the abundances of common species. At small spatial scales, forest quality and topographic roughness were significant determinants of beta-diversity. In unlogged forest, analysis of beta-diversity revealed sites of distinct ecological communities relevant to some that appeared to be defined by microclimate. At larger scales, spatial turnover in community composition was the strongest contributor to diversity followed by habitat structure, microclimate and then topography. Oil palm plantations are of low value and large areas of unlogged forest are evidently of highest value for the conservation of biodiversity. Degraded forest retains remarkable diversity through shifts in the spatial arrangement of ecological communities, and thus I recommend that small areas of even heavily-logged forest should be preserved where they are created in agricultural matrices. Future studies on land-use change in Borneo should incorporate beta-diversity into their designs as the component reveals mechanisms by which diversity loss might be mitigated.