BACKGROUND: In recent years, the downward trajectory of malaria transmission has slowed and, in some places, reversed. New tools are needed to further reduce malaria transmission. One approach that has received recent attention is a novel house-based intervention comprising window screening (S) and general house repairs to make the house more mosquito proof, together with EaveTubes (ET) that provide an innovative way of targeting mosquitoes with insecticides as they search for human hosts at night. The combined approach of Screening + EaveTubes (SET) essentially turns the house into a 'lure and kill' device. METHODS: This study evaluated the impact of SET on malaria infection prevalence in Côte d'Ivoire and compares the result in the primary outcome, malaria case incidence. Malaria infection prevalence was measured in a cross-sectional survey in 40 villages, as part of a cluster-randomised trial evaluating the impact of SET on malaria case incidence. RESULTS: Infection prevalence, measured by rapid diagnostic test (RDT), was 50.4% and 36.7% in the control arm and intervention arm, respectively, corresponding to an odds ratio of 0.57 (0.45-0.71), p < 0.0001). There was moderate agreement between RDT and microscopy results, with a reduction in odds of infection of 36% recorded when infection was measured by microscopy. Prevalence measured by RDT correlated strongly with incidence at a cluster level. CONCLUSIONS: In addition to reducing malaria case incidence, house screening and EaveTubes substantially reduced malaria infection prevalence 18 months after installation. Infection prevalence may be a good metric to use for evaluating malaria interventions in areas of similar transmission levels to this setting. TRIAL REGISTRATION: ISRCTN18145556, registered 1 February 2017.