Microbial diversity may affect host phenotypes, including morphology and behaviour, but it remains unclear to which extent those could be mediated by host differences in diet or habitat use. We used a population of wild common waxbills living in a large open-air mesocosm to control for such differences and test whether phenotypic variation is associated with cloaca bacteria diversity. We also tested correlations between feather-associated bacteria diversity and plumage colour ornamentation. Albeit weakly correlated, individuals sharing more similar cloaca microbiotas were more similar in their carotenoid-based plumage and bill red colour, suggesting that the gut microbiota can influence ornamentation even when individuals are in the same habitat and have access to the same food resources, perhaps mediating individual differences in feeding or digestion. There were no associations between feather bacteria and plumage colour, nor between cloaca bacteria and body size or several behavioural phenotypes. These results further highlight that investigating associations between microbiota and behaviour in nature should account for variation in extrinsic factors.