Updated publication reference for PubMed record(s): 32184257. The malaria parasite, Plasmodium falciparum, traffics the virulence protein P. falciparum erythrocyte membrane protein 1 (PfEMP1) to the surface of infected red blood cells (RBCs) via membranous organelles known as the Maurer’s clefts. We developed a method for efficient enrichment of Maurer’s clefts and profiled the protein composition of this trafficking organelle. We identified 18 previously uncharacterised or poorly characterised Maurer’s cleft proteins. Transfectants expressing GFP-fusions of 7 of these proteins and confirmed their Maurer’s cleft location. Co-immunoprecipitation and mass spectrometry identified interacting partners of these Maurer’s clefts proteins, providing a network map of protein-protein associations. We identified two key clusters of proteins that may function in the loading and unloading of PfEMP1 into and out of the Maurer’s clefts.