Measurement of faecal hormonal metabolites has become a widespread method in field endocrinology due to its non-invasiveness and ability to assess long-term stress; however, this approach has some limitations. We tested the potential of this assay for the Daubenton's bat (Myotis daubentonii), a small vespertilionid species (body mass 6–10 g), and we explored the relationship between cortisol and testosterone levels and dawn swarming, a signalling behaviour that occurs during roost-switching. Swarming was recorded using automated PIT-tag readers on the tree roosts of a maternity colony. In spite of absence of biological validation, our preliminary results demonstrate that field conditions of sample storage and small faeces weight do not interfere with hormonal measurement. We also found a positive correlation between individual levels of stress hormone (cortisol faecal metabolites) and swarming behaviour, but this should be interpreted with caution due to methodological shortcomings that need to be improved in future studies.