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Microbiome constitutes an important axis of individual variation that, together with genes and the environment, influences an individual's physiology and fitness. Microbiomes are dependent not only on an individual's body condition but also on external factors, such as diet or stress levels, and as such can be involved into feedbacks between the external ecological factors and internal physiology. In our study, we used a wild population of blue tits Cyanistes caeruleus to investigate the impact of external habitat composition on the microbiome of adult birds. We hypothesized that – through differences in plant composition, potentially affecting diet complexity – habitat type may impact the diversity and structure of the gut microbiome. Blue tits breeding in dense deciduous forests tended to have more diverse microbiomes and be significantly different in terms of microbiome composition from birds breeding in open, sparsely forested hay meadows. Distinct study plots also tended to differ in a number of parameters describing microbiome diversity. We observed no microbiome differentiation according to individual characteristics such as sex or age. The study emphasizes that external environment is one of the important modulators of microbiome diversity and calls for more such studies in wild animal populations.