As colonially breeding species, seabirds have the potential to suffer from transmissible infectious agents (IAs), such as avian cholera or highly pathogenic avian influenza. Those threats come on top of other well-identified factors, such as introduced species, climate change and fishery activities. Understanding eco-epidemiological processes in wildlife populations requires a combination of complementary information, starting from detecting the occurrence of IAs among host populations. To efficiently complete investigations on field samples from vertebrate populations on subantarctic islands, we developed a microfluidic high-throughput technique to perform 48 simultaneous real-time PCRs to detect a set of a priori selected IAs on 48 samples. This low-cost, versatile, DNA-saving system enables screening for multiple parasites on numerous samples, providing a tool to get first snapshots of patterns of exposure to IA before further investigation. We describe its application to perform a multi-parasite, multi-host, multi-scale analysis on vertebrate populations of the South Indian Ocean. We analysed 450 samples from healthy seabirds including high-density breeding species (like the Indian yellow-nosed albatross (Thalassarche carteri) or spheniciforms), scavengers (such as giant petrels (Macronectes giganteus and M. halli)), burrowing white-chinned petrel (Procellaria aequinoctialis) and from native (pinnipeds) or introduced (rats, mice) mammals. We also included necropsy samples from a passive surveillance programme. The most commonly detected bacteria of the Chlamydiaceae family (prevalence up to 70% in some colonies), Pasteurella multocida and Erysipelothrix amsterdamensis, whose presence was previously known only on certain islands. These results open important perspectives for disease ecology and seabirds conservation.