Human genetic diversity can reveal critical factors in host-pathogen interactions. This is especially useful for human-restricted pathogens like serovar Typhi ( Typhi), the cause of typhoid fever. One key defense during bacterial infection is nutritional immunity: host cells attempt to restrict bacterial replication by denying bacteria access to key nutrients or supplying toxic metabolites. Here, a cellular genome-wide association study of intracellular replication by . Typhi in nearly a thousand cell lines from around the world-and extensive follow-up using intracellular Typhi transcriptomics and manipulation of magnesium availability-demonstrates that the divalent cation channel mucolipin-2 (MCOLN2 or TRPML2) restricts Typhi intracellular replication through magnesium deprivation. Mg currents, conducted through MCOLN2 and out of endolysosomes, were measured directly using patch-clamping of the endolysosomal membrane. Our results reveal Mg limitation as a key component of nutritional immunity against Typhi and as a source of variable host resistance.