Harvesting of products from plants in the wild is widespread throughout southern Africa. Particularly important products are plant parts used in traditional medicine. However, the impacts of harvesting practices are rarely quantified, with as yet insufficient generic rules across species and life forms. This limits the predictive ability to monitor and manage the affected populations. This paper examines the harvesting impact on two popular woody medicinal species used throughout sub-Saharan Africa, namely Catha edulis (Vahl) Forssk. ex Endl. (bushman’s tea) and Rapanea melanophloeos (L.) Mez. (Cape beech). In both species, basal diameters, heights, and the number of size classes in the harvested populations were lower than in unharvested. Densities of harvested populations were higher in both species, including densities of young plants, but the frequency of individuals in larger size classes was lower. The populations of both species being harvested for medicinal products appeared to be withstanding the current levels of harvesting, but the population structure of C. edulis populations being harvested for poles on the roadside and near human settlements had been substantially altered. Despite the resilience of the two species to harvesting for medicinal products, loss of habitat or changes in land use pose a threat to a number of the assessed populations.