The biodiversity–ecosystem functioning (B–EF) relationship has become of main interest in the last few decades, mostly because of the worldwide increase in species extinctions. However, most of these studies only consider species within single size-class or trophic level, thereby most likely underestimating ecosystem complexity. To reach more realistic scenarios, we assessed the role of meiofauna (lower size-class level) on the relationship between macrofaunal biodiversity and multiple benthic ecosystem properties. Experiments took place under controlled conditions using three macrofaunal species (Alitta (formerly Nereis) virens, Macoma balthica and Mya arenaria). A total of eight combinations of zero to three functionally different macrofaunal species were maintained in microcosms for 34 days in either the presence or absence of a different size-class grouping (a meiofaunal mixture). The organic matter content and bacterial abundance in sediments and the oxygen and nutrient (NH4+, NOx-, PO4 3-) fluxes across the sediment-water interface were measured and used as proxies of ecosystem properties. Overall, macrofaunal species richness did not modify any of the measured properties; however, we observed changes associated to the presence of A. virens and M. balthica. This study also revealed a strong impact of the presence of meiofauna on ecosystem properties. They changed interactions between macrofaunal species, which led to modifications in the ecosystem properties. Thus, even if this size-class group has been poorly considered in previous studies, this experiment suggests that future studies should consider the meiofauna with greater attention, particularly in the context of B–EF.