People can develop immunity to malaria following repeated exposure; hence the global search for a vaccine. However, it remains unclear how immunity is acquired. We propose that immunity to Plasmodium falciparum malaria requires specific types of humoral and cell-mediated cooperation, in particular merozoite opsonisation and memory CD4 T cell effector functions. We have investigated our model in longitudinal human population studies from Papua New Guinea (PNG) using in vitro assays of functional immunity. Novel whole-parasite techniques were developed to quantify merozoite opsonisation and functional CD4 T cell memory by 16-parameter flow-cytometry, and data related to clinical and parasitological outcomes. We have identified merozoite opsonisation as a strain-transcending definitive correlate of protective immunity, with up to a 85% decrease in risk of clinical malaria observed. We have measured the frequency, magnitude and breadth of CD4 memory responses to merozoites, including production of IFNγ, TNF and IL-10 and poly- functional T cells. In what is the most comprehensive study of its kind to date, investigating humoral and cell-mediated mechanisms has enabled us to build a detailed model of natural immunity and has identified novel biomarkers that will assist the evaluation of future vaccines.