Although gastrointestinal helminths have a high prevalence in non-human primates (NHPs), there is still a large lack of knowledge about their interactions with climate-driven seasonal patterns, particularly in tropical rainforests. Using gastrointestinal dissections from 11 free-ranging NHP species (N = 190 individuals) donated by indigenous subsistence hunters, we investigated gastrointestinal helminth infections in two areas in the northeastern Peruvian Amazon. Helminth richness included seven nematodes, two cestodes, and one acanthocephala. Parasites were detected in 85.3% of NHPs, with the most common helminth taxa identified being Physaloptera dilatata, Trypanoxyuris sp., Strongyloides cebus, Molineus torulosus and Prosthenorchis elegans. We obtained data on helminth occurrence, diversity, and location within the gastrointestinal tract and parasite-induced histopathological lesions. Significant differences in parasitic indicators in relation to seasonal variations in climate, particularly temperature and water levels. These findings provide valuable insights into the helminth infection dynamics of free-ranging primates in the Amazon, highlighting key parasite-host relationships and their pathological impacts. This study contributes to our understanding of primate health and parasite ecology in a highly biodiverse region and provides valuable information for understanding the potential consequences of global warming on the transmission of parasitic infections.