While the direct toxicological effects of metal exposure on animals, including birds, are well documented, indirect mechanisms remain poorly understood. This applies to effects on microbiota, despite the emerging evidence of its crucial role in host's physiological functions. We investigated the metal exposure, growth, and fledging of great tits (Parus major) in six rural vs. industrial/urban area (IUA) comparisons across Europe to identify associations with bird gut microbiota. To capture a range of pollution profiles, IUAs included both city settings and industrial sites such as a copper-nickel smelter, a metallurgical plant, a pulp mill, and a lead mine. Fecal samples from 191 broods were analyzed for bacterial 16S rRNA and concentrations of 18 elements, of which nine common contaminants were selected for further analyses. Nestlings in IUAs showed higher metal exposure than those in rural sites, except near a pulp mill, with opposing results. An index describing impervious land cover was a weak predictor for most microbiota metrics. Instead, the rural vs. IUA comparison potentially caught the environmental characteristics better, showing effects on the fledgling number, body mass, microbial composition, and abundances of several taxa, though these patterns were location dependent and may reflect secondary effects of pollution, like changes in habitat quality and diet. Taxa with links to both metal levels and nestling performance were identified. Despite reduced emissions in Europe, wild birds remain exposed to metal pollution, particularly near industrial areas. Overall, our findings suggest that anthropogenic influence associates with wildlife microbiomes and health in a context-dependent manner.