The amphibian skin microbiome is a key component of the host’s innate immune system. However, we lack a complete understanding of the mechanisms by which different drivers can alter this function by modulating the microbiome’s structure. Our aim was to assess the extent to which different host attributes and extrinsic factors influence the structure of the skin microbiome. Skin bacterial diversity was examined in 148 individuals of the four-eyed frog (Pleurodema thaul) from 16 localities spanning almost 1,800 km in latitude. Alpha (richness) and beta diversity and abundance of bacterial amplicon sequence variants were used to describe its structure. Predictors associated with the host (developmental stage, genetic lineage, individual Batrachochytrium dendrobatidis [Bd] infection status) and the landscape (current climate, degree of anthropogenic disturbance) were used in the statistical modelling in an information theoretical approach. Bd infection and host developmental stage were the only predictors affecting microbiome richness, with Bd+ individuals and adults and juveniles having higher richness than Bd- ones and tadpoles, respectively. High diversity in Bd+ individuals is not driven by bacterial families with known anti-Bd properties. Beta diversity was not affected by Bd infection and is mostly a consequence of bacterial family turnover, rather than nestedness. Finally, for those bacterial families that are known to have inhibitory effects on chytrid, Bd- individuals are slightly more diverse than Bd+ ones. Our study confirms an association between Bd infection and the host developmental stage with the skin microbiome of P. thaul. Unexpectedly, macroclimate and human impact factors do not seem to play a role in shaping the amphibian skin microbiome. Our study exemplifies that focusing on a single host-parasite system over a large geographic scale can provide important insights into the factors driving host-parasite-microbiome interactions.