Gastro-intestinal helminths are present in nearly all mammals, sharing their environment with microbiota. Gastro-intestinal helminth-microbiota associations are shaped by various ecological processes and can influence their host’s health. However, the effect of the ecological context of the host in terms of geographic location, seasonality, and anthropogenic effects (i.e., logging history) on both groups of gastro-intestinal inhabitants is unknown. We provide a first exploration thereof, and also on the interactive effects between gastro-intestinal helminths and microbiota. Fresh faecal samples (N= 338) from eight wild Eulemur populations were collected over a 2-year period across Madagascar in a diversity of habitats. We used 16S ribosomal RNA gene sequencing to characterise the microbiota composition, and faecal flotation to isolate and morphologically identify nematode eggs. Infections with nematodes of the genera Callistoura and Lemuricola occurred in all lemur populations. Seasonality significantly contributed to the observed variation in microbiota composition, especially in the dry-deciduous forest. We found indications that differences in nematode prevalence were larger in (western) dry-deciduous forests compared to (eastern ) rainforests. Both microbial richness and Lemuricola spp. infection prevalence were highest in a previously logged site, whereas the prevalence of Callistoura spp. was highest in the less intensely logged site. In addition, we observed significant correlations between gastro-intestinal parasites and microbiota composition in wild these lemurs. We furthermore show that environmental conditions affect gastro-intestinal nematodes and microbial interactions in ways that, as far as we know, have not previously been reported and that may also be of relevance for lemur conservation.