This dataset comprises individual-level data from 67 participants in the POPVAC A and POPVAC C randomised controlled trials. POPVAC A was conducted among schoolchildren from Koome islands, Uganda (a schistosomiasis-endemic setting). POPVAC C was undertaken in Entebbe municipality among participants of the Entebbe Mother and Baby Study (EMaBS) cohort. Variables include data on socio-demographic characteristics, S. mansoni infection, and immune cluster frequencies (cell counts as a proportion of total live CD45+ PBMCs per sample) from mass cytometry experiments conducted on peripheral blood mononuclear cells from POPVAC participants.