Intensive farming leading to landscape homogenization and massive use of pesticides is threatening biodiversity associated with agricultural landscapes. Pesticides may alter the composition of gut microbiota, which contributes critically to a variety of host metabolic and immune functions, and the consequences on wildlife health are still unknown. We studied potential effects of farming practices on the gut microbiota of wild populations of Iberian hare (Lepus granatensis) inhabiting conventional (synthetic pesticide-treated, mostly glyphosate) and organic (synthetic pesticide-free) farming areas in Central Spain. We analyzed duodenum, caecum, and rectum sections and fresh feces by massive 16S rRNA gene sequencing. Our study supports the use of fresh feces as a non-invasive proxy for monitoring dynamic changes of the gut community. The gut metacommunity in conventional fields showed higher richness and diversity (both ecological and phylogenetic) but with more homogeneous composition among hares (lower beta-dispersion) than the gut metacommunity detected in organic farming areas. We did not observe dysbiosis or significant enrichment in pathogenic bacteria. Potential negative effects on community-level abilities for vegetable fiber degradation and butyrate metabolism were observed in conventional areas. Ruminococcaceae, which play a key role as cellulose degraders, showed significant lower relative abundances in conventional fields. We show a gut index based on the ratio of fecal Ruminococcaceae that may be helpful for predictive environmental diagnostic. Further experimental research and in situ monitoring of gut microbiota are needed to substantiate these findings and to fully understand the potential undesired effects of the use of synthetic pesticides in untargeted wildlife.