African forests are under increasing pressure to supply local, regional, and international demand for timber. Much of this trade is unregulated, such that there is increasing concern regarding the ecological sustainability of this resource use. However, there is a lack of studies investigating the ecological impact of informal timber harvesting in African forests. While forest species have adapted to natural canopy gap dynamics, harvesting may alter natural disturbance regimes, with adverse effects on biodiversity. Information regarding harvest gaps, and concomitant impacts on habitat and biodiversity is thus essential to inform sustainable management. This study compared the frequency and nature of harvest gaps and natural gaps in a coastal forest in the Eastern Cape, South Africa, where informal selective timber harvesting occurs. Habitat condition and bird species richness and composition were compared across intact forest, natural gaps, and harvest gaps. Harvest-created gaps increased the number of canopy gaps by 30%, but were comparable with natural gaps in size. Habitat conditions in harvest gaps represented an intermediate state between intact forest and natural gaps, thereby increasing forest-scale habitat heterogeneity. While bird species richness was not affected, species composition differed across intact forest, harvest gaps and natural gaps, driven by changes in habitat condition, and mediated by species’ feeding and nesting traits. Specifically, insectivores, cavity- and ground-nesting species, and hawking and arboreal probing species were negatively affected by the habitat gradient from intact sites to canopy gap conditions, while nectarivores, omnivores and ball/cup nesting species were positively affected. Thus, while the single-tree selective harvesting method used by informal harvesters largely emulated natural canopy disturbances, the harvest-mediated increase in the frequency of canopy gaps may reduce the abundance of certain bird species sensitive to canopy gap conditions and reduce forest-scale beta-diversity.