Metazoans contributed historically to the decline of the microbialites and continue to restrict their formation in most modern environments through grazing and burrowing pressures. Recent evidence suggests that metazoans can coexist with layered microbialites (stromatolites). However, the possible drivers of the invertebrate assemblage directly associated with these unique habitats are not well-understood. This study measured environmental and resource variables within peritidal stromatolites along the South African coastline and related these to the infaunal metazoan community. Clitellates (Naididae and Enchtraeidae), malacostracans (Amphipoda, Isopoda and Tanaidacea), insect larvae (Chironomidae), and polychaetes (Nereididae) were the most abundant groups. The benthic macrofaunal community was most strongly related to salinity, nutrients (dissolved inorganic nitrogen and phosphorus) and macroalgal cover. This suggests that the distribution of some species was restricted by physiological tolerances associated with salinity, while others responded to resource variability within the primary producer community. The absence of an apparent relationship between stromatolite microalgal biomass or composition and the metazoan community occupying the matrix indicates that the invertebrates might be relying on other primary producers as a food resource, such as macroalgae. This suggests that the benthic macrofaunal community may have a limited direct grazing effect on the stromatolite matrix, thereby not hindering the formation of its typical layered fabric.