Pollinator diversity and abundance are declining in the agricultural landscapes of some parts of the world along with the pollination services they provide. Among an array of reasons, climate change has been pointed out as a major player and studies suggest strong negative impacts on agricultural pollination toward the end of the 21st century. In this study, we investigated for the first time the concomitant effect of climate changes on a tropical crop, passion fruit (Passiflora edulis), and its two main pollinator bee species (Xylocopa frontalis and X. grisescens) in the Neotropics considering two of the IPCC environmental scenarios, RCP 4.5; RCP 8.5 (Representative Concentration Pathways), and in the years 2060 and 2080. We have shown that the climate changes may lead to changes in the natural ranges of Xylocopa bees, with considerable loss of habitable area (X. frontalis, RCP 4.5 = −27.3 to −15.4%; RCP 8.5 = −57.7 to −47.9%; X. grisescens, RCP 4.5 = −15.4 to −27.81%; RCP 8.5 = −23.5 to −35.3%), as well as for cropping passion fruit (RCP 4.5 = −44. 9 to −51.3%; RCP 8.5 = −42.9 to −64.8%), for years 2060 and 2080, respectively. We also predicted a potential reduction between 31.9% and 54.9% in the overlapping of the remaining suitable areas for the bees and passion fruit, increasing the potential spatial mismatch between the crop and its pollinators. Based on the models forecast of climate changes, we conclude that the suitable areas to co-occurrence of passion fruit crop and its effective pollinators will be largely affected in the Neotropics and steps to mitigate the effects of the climate changes should be taken to ensure viable population of pollinators in the remaining suitable areas for both bees and the crop.