The prevalence of malaria parasite species in parts of Africa is rapidly changing and influenced by detection methods. tThe natural vector competence and vectorial capacity of African anophelines for human Plasmodium species has only been well described for P. falciparum and is unclear in the context of mixed and non-falciparum infections. Over the course of two clinical trials (2015 and 2019-2020) testing ivermectin for malaria control in the same region of Burkina Faso, we sampled participants blood and their households for Anopheles spp. mosquitoes and tested these samples for Plasmodium species. Plasmodium prevalence in participants and their blood samples was high in both trials. While only P. falciparum mono-infections were detected in the 1st trial, mixed and non-falciparum infections comprised 27% of infections in the 2nd trial, with notable changes in species present within participants over time. Furthermore, An. gambiae s.l. was the main vector captured, but An. funestus mosquitoes were unexpectedly prevalent in the 2nd trial, and we found that parasite species prevalence differed in abdominal and head+thorax tissues of these two vector species. Most notably, P. falciparum sporozoites were significantly more prevalent han other parasite species in An. gambiae s.l. t while P. ovale sporozoites were significantly more prevalent than other parasite species in An. funestus. Our data suggest differential vector competence for Plasmodium species at the study site, which may significantly impact malaria epidemiology, disease prevalence and control efforts.