As invasive plant species are a major driver of change on oceanic islands, their control is an important challenge for restoration ecology. The post-control recovery of native vegetation is crucial for the treatments to be considered successful, but few studies have evaluated the effects of control measures on both target and non-target species. To investigate the efficiency of manual control of Cinchona pubescens and its impacts on the sub-tropical highland vegetation of Santa Cruz Island, Galápagos, vegetation was sampled before and up to two years after control was carried out in permanent sampling plots. Manual control significantly reduced Cinchona density. Due to regeneration from the seed or bud bank, follow-up control is required, however, for long-term success. Despite heavy disturbance from tree uprooting, herbaceous angiosperms were little affected by the control actions, whereas dominant fern species declined in cover initially. Most native, endemic, and other introduced species regained their pre-control levels of cover 2 years after control; some species even exceeded them. The total number of species significantly increased over the study period, as did species diversity. The native highland vegetation appeared to be resilient, recovering to a level probably more characteristic of the pre-invasion state without human intervention after Cinchona control. However, some introduced species seemed to have been facilitated by the control actions, namely Stachys agraria and Rubus niveus. Further monitoring is needed to confirm the long-term nature of vegetation change in the area.