The datasets here are a key addition to the Malaria Cell Atlas, that include short and long read single cell RNA-sequencing profiles of i) over 37,000 Plasmodium falciparum cells across intraerythrocytic asexual and sexual development of laboratory strains ii) ~1000 P. falciparum parasites collected from an asymptomatic Malian individual naturally infected with multiple strains. A single cell atlas comprising the laboratory dataset as well as an integrated atlas of both laboratory and field strains is generated and provided as a data resource to the malaria research community at malariacellatlas.org