The gut microbiome is an important mediator of life-history traits in animals and performs essential functions that may allow hosts to exploit novel niches. However, sources of variation in microbiome abundance and composition within vertebrate species are poorly understood, particularly in wild birds. Here we used 16S rRNA gene sequencing to describe the faecal microbiome of a trans-Saharan migratory passerine species breeding in Central Spain, the European Pied Flycatcher Ficedula hypoleuca. We investigated differences in microbial composition and diversity between the natural habitat of the species (oak forest) and a newly created habitat (pine forest) located only 1km apart. We sampled both adult males and females, as well as nestlings (13 days old). The results showed a difference in the composition of microbiomes of birds between the habitats, with birds from the oak forest showing a higher abundance of bacterial taxa, such as Actinobacteriota and Proteobacteria, and birds from the pine forest showing a higher abundance of Verrucomicrobiota. We observed no differences in microbial composition according to sex or age, although nestlings and breeding females showed a higher abundance of certain bacteria, especially in the oak forest. We also investigated differences in metabolic functions of the microbiome and detected a higher relative abundance of bacteria with fatty acid biosynthesis and degradation pathways, as well as metabolite precursor and energy generation pathways in birds from the oak forest. In the pine forest, we found a higher abundance of bacteria with the L-alanine biosynthesis and pentose phosphate pathways. Our study improves our understanding of the gut microbiome composition of insectivorous migratory passerines and shows that breeding habitat can be a key modulator of avian gut microbiome composition.