In recent decades, agriculture has intensified to meet growing demand and boost productivity. So-called conventional farming involves increased use of pesticides, which are now omnipresent in the environment. Due to their wide distribution and lack of specificity, non-target organisms, such as farmland birds, can be exposed to them in a variety of ways (water, food, etc.). Today, these individuals are exposed to sub-lethal doses of many pesticides, recognised as a major factor in the decline of birds. On the other hand, organic farming, which excludes pesticides, limits this exposure and can promote biodiversity. The effects of pesticides on the physiology of birds are well documented, but the role of the gut microbiota as a modulator remains little studied. As ingestion is the main path of exposure, the gut microbiota may be directly affected. Involved in the absorption of nutrients, its composition and diversity could be altered, with negative or beneficial effects on immunity. It is therefore essential to gain a better understanding of the factors influencing these interactions. The aim of this study was to assess the impact of a feeding with or without pesticides on the gut microbiota and physiology of captive Grey partridges (Perdix perdix), by comparing two groups fed either organic or conventional grain. Cloacal samples were taken at the beginning and end of the experiment to analyse the microbial diversity and taxonomic composition of each individual. Alpha diversity, reflecting individual microbial diversity, was assessed using species richness and the Shannon index. Beta diversity, comparing communities between individuals, was analysed using the Bray-Curtis and Jaccard indices. The results show that microbial diversity did not differ according to feed, but decreased over time in females. Microbial communities' structure was not influenced by feed, although a slight diversification was observed at the end of the experiment in males fed on conventional grain. These results reveal complex interactions between feed, microbiota and physiology, underlining the importance of continuing research to better understand these relationships, both for wildlife and for human health.