Background <p>Mixed-species, mixed-strain plasmodia infections are known to occur in humans in malaria endemic areas. It may be surprising that to date, the extent of this complexity has not been systematically explored in high-burden countries of sub-Saharan Africa, especially in the reservoir of asymptomatic infections in all ages, which sustains transmission.</p> Methods <p>Here we take a metagenomic lens to these infections by sampling variable blood volumes from 188 afebrile residents living in high, seasonal transmission in Northern Sahelian Ghana. We estimated multiplicity of infection for different <i>Plasmodium</i> spp. through genotyping of antigens and microsatellites. We further defined ‘metagenomic complexity’ as a measure of overall within-host complexity across the combination of species and strains.</p> Results <p>We show that prevalence of <i>Plasmodium</i> spp. and inter-/intra-species complexity is significantly higher in larger blood volumes from these individuals. Overall, malaria infections display high levels of metagenomic complexity comprising single-, double-, and triple-species infections with varying levels of intra-species complexity for <i>P. falciparum, P. malariae, P. ovale curtisi, and P. ovale wallikeri</i>. We also report a subset of individuals with highly-complex infections that cannot be explained by age or location. The implications of these findings to malaria epidemiology and control are illustrated by a geographic scaling exercise to district and region levels in northern Ghana.</p> Conclusions <p>Our metagenomic investigation underscores the need to more sensitively measure within-host <i>Plasmodium</i> spp. complexity in asymptomatic carriers of infection. This will optimise strategies for malaria surveillance and control.</p>