The close evolutionary relationship and similar physiology of non-human primates and humans mean that they can share many pathogens. Historic long-term data and field studies in Uganda and the Côte d’Ivoire provide insights into the cascading impacts of environmental changes on non-human primate behaviour, ecology and microorganism transmission. I will present data showing that red colobus monkey (Procolobus rufomitratus) group sizes increased on a parkwide scale in Kibale National Park and had cascading impacts on other behaviours including activity budgets, diets, and competitive regimes in these groups. I present our research showing that flies actively track monkeys and carry infectious bacterial pathogens, and that these associations represent an understudied cost of sociality, with higher fly densities associated with larger group sizes. I present research on factors influencing the structure of bacterial gut microbiomes and the bacteriophages that influence these communities in these changing environments and show evidence for co-evolution of some phages with their primate super-hosts and zoonotic transmission of phages from humans to primates living in captivity. I will present our use of hybridization capture coupled with next generation sequencing on a diversity of substrates including tissues, flies, and bones, which enable research on wild primate pathogens like Treponema pallidum pertenue, the pathogen responsible for human yaws disease, Bacillus cereus biovar anthracis, causing sylvatic anthrax, and a diversity of viruses. Lastly, I present evidence that flies are a tool for biomonitoring, providing information on the mammals and pathogens present in ecosystems that may help us study their populations at large scales.