Malaria-causing Plasmodium parasites undergo multiple phenotypic transitions as they cycle between diverse niches in the mammalian and mosquito hosts. Recent applications of single-cell technologies to Plasmodium have enabled the systematic investigation of the distinct stages across the life cycle. Most single-cell data have focused on the parasite exclusively, but a few studies have started to profile both parasite and host cells to shed light on the heterogeneity of cell states that underpin host-parasite interactions. In this opinion article, we highlight how atlasing initiatives are starting to be used to infer functional interactions between parasite and host and could be a powerful tool in drug discovery and vaccine development.