Abstract Impacts of plant invasions are largely scale-dependent and responses to the same exotic species may vary among communities. Since impacts caused by individual trees could anticipate consequences of a closed canopy of an invader, we studied the response of Galapagos native plants to quinine (Cinchona pubescens) trees in two vegetation zones. Quinine has invaded >11,000 ha of Santa Cruz Island, including the Miconia- and Fern-Sedge-Zones. We analysed species composition and abundance along transects radiating from the trunks of individual quinine trees. Species richness and percentage cover decreased significantly with proximity to individual trees, and these effects were more pronounced in the Fern-Sedge Zone than in the Miconia Zone. Cover of endemic and native herb species and grass species significantly declined by 57–88% in the Fern-Sedge Zone. This was not the case in the Miconia Zone, but here the dominant endemic Miconia robinsoniana decreased by 41%. Quinine is a major driver of plant community change in both vegetation zones. The greater susceptibility of species in the Fern-Sedge Zone was ascribed to the presence of a new growth form: quinine trees in a formerly treeless environment. Species of the Miconia Zone appeared to be better pre-adapted to higher shade levels created by the Miconia shrubs. Our results emphasize the need for future control of quinine to preserve the diversity of the native Galapagos flora.