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Protected areas (PAs) are a cornerstone to biodiversity conservation, reducing the negative effects of human occupation on the biodiversity persistence. However, the implementation of PAs does not always mitigate the impacts of human occupation such as biological invasions and climatic changes. We evaluated the effect of the invasion of Artocarpus heterophyllus, the jackfruit, over Atlantic Forest PAs, under the influence of climate changes and across scales. The environmental suitability of jackfruit for preindustrial, future (2080), and delta (=future-preindustrial) was used to establish the risk of invasiveness. To validate the hypothesis that PAs have higher jackfruit invasiveness than usual in preindustrial, future, and delta periods, we used a null model. We conducted a phytosociological study in Guariru Natural Heritage Private Reserve (NHPR) for evaluating the effect of jackfruit on species richness. The Atlantic Forest PAs have higher jackfruit environmental suitability than expected for both preindustrial, future, and delta periods. In Guariru NHPR, the presence of jackfruit was inversely proportional to the species richness. The combined effect of jackfruit invasion and climatic changes showed that the Atlantic Forest PAs are threatened by the effect of jackfruit competitive pressure over native species, thus dominating ecosystems both by density and biomass, in preindustrial, and under climate changes. Guariru NHPR is already losing its biodiversity through the presence of jackfruit, needing management interventions. We strongly recommend that to combat the occurrence of jackfruit in Atlantic Forest PAs, management interventions should be taken to control its persistence, also delineating its role inside the community structure.