The molecular force of blood-stage infection (_molFOB) is a quantitative surrogate metric for malaria transmission at population level and for exposure at individual level. Relationships between _molFOB, parasite prevalence and clinical incidence were assessed in a treatment-to-reinfection cohort, where P.vivax (Pv) hypnozoites were eliminated in half the children by primaquine (PQ). Discounting relapses, children acquired equal numbers of new P. falciparum (Pf) and Pv blood-stage infections/year (Pf-_molFOB = 0-18, Pv-_molFOB = 0-23) resulting in comparable spatial and temporal patterns in incidence and prevalence of infections. Including relapses, Pv-_molFOB increased >3 fold (relative to PQ-treated children) showing greater heterogeneity at individual (Pv-_molFOB = 0-36) and village levels. Pf- and Pv-_molFOB were strongly associated with clinical episode risk. Yearly Pf clinical incidence rate (IR = 0.28) was higher than for Pv (IR = 0.12) despite lower Pf-_molFOB. These relationships between _molFOB, clinical incidence and parasite prevalence reveal a comparable decline in Pf and Pv transmission that is normally hidden by the high burden of Pv relapses.