Research on crop systems and biodiversity conservation in the tropics has mainly been concerned with how low to mid intensity agricultural systems can benefit from adjacent natural habitats by receiving ecosystem services from natural biodiversity. One intensively studied crop in this framework is coffee. Positive effects are relatively easy to quantify by comparing coffee yield and by recording native species diversity. However, a largely overlooked issue is how agricultural areas affect native organisms in adjacent habitats, for example through movement of pest species that could impose a risk of degrading these habitats. We give an example from Mauritius, where an introduced coffee pest severely reduces the reproductive success of a threatened endemic plant species. We argue that such effects may be more common than suggested by the literature, especially when crop and native plants are congeneric. In the long term, such negative effects may degrade natural habitats, thereby causing ecosystem services derived from these habitats to decline.