During a longitudinal study investigating the dynamics of malaria in Ugandan lakeshore communities, a consistently high malaria prevalence was observed in young children despite regular treatment. To explore the short-term performance of artemether-lumefantrine (AL), a pilot investigation into parasite carriage after treatment(s) was conducted in Bukoba village. A total of 163 children (aged 2-7 years) with a positive blood film and rapid antigen test were treated with AL; only 8.7% of these had elevated axillary temperatures. On day 7 and then on day 17, 40 children (26.3%) and 33 (22.3%) were positive by microscopy, respectively. Real-time PCR analysis demonstrated that multi-species Plasmodium infections were common at baseline, with 41.1% of children positive for Plasmodium falciparum/Plasmodium malariae, 9.2% for P. falciparum/ Plasmodium ovale spp. and 8.0% for all three species. Moreover, on day 17, 39.9% of children infected with falciparum malaria at baseline were again positive for the same species, and 9.2% of those infected with P. malariae at baseline were positive for P. malariae. Here, chronic multi-species malaria infections persisted in children after AL treatment(s). Better point-of-care diagnostics for non-falciparum infections are needed, as well as further investigation of AL performance in asymptomatic individuals.