Mobile metazoans in the Phanerozoic transformed shallow coastal habitats covered in biofilms into bioturbated mixed grounds. Benthic biofilms during this time rarely preserved into the fossil record as microbialites, and more specifically their layered form, stromatolites. Living microbialites are rare for this reason, in addition to other factors such as unfavourable modern geochemical conditions. Counterintuitively, macroinvertebrate grazers and laminated stromatolites coexist along the Nelson Mandela Bay coastline, South Africa. Here we aimed to determine if nutritional qualities of algae in these microbialite pools are linked to the diet of a dominant amphipod grazer, Melita zeylanica Stebbing, 1904. We assessed this in 3 microbialite pools using stable isotopes coupled to seasonal shifts in abundant food resources of microbialite biofilms and exposed (bleached and rimstone) or submerged (pool) macroalgae, Ulva spp. Amphipod diet was proportional to the quantity available (biomass) and nutritional properties of available algal food (energy, protein, total phosphorus and C:N ratios). Macroalgae in all states were the most nutritious, and the diet of M. zeylanica was dominated by submerged macroalgae. Although microbialite material had the worst nutritional profile, it was consumed in larger quantities compared to exposed bleached and rimstone macroalgae. Therefore, factors unrelated to nutritional profiles, such as predation, allelopathy or exposure risks, likely drive food choices. High levels of grazing on nutritious pool macroalgae likely releases most of the grazing pressure on the microbialite biofilm, therefore partially explaining why the microbialites can persist in this environment instead of being bioturbated through foraging.