In most vertebrate animals, glucocorticoid hormones are the chief mediators of homeostasis in response to ecological conditions and as they progress through their lifecycle. In addition, glucocorticoids are a major part of the stress response and stress induced elevations of the hormone can make it difficult to assess glucocorticoid secretion in response to changes in life-stage and current environmental conditions in wild animals. Particularly when quantifying circulating levels of glucocorticoids in the blood which fluctuate rapidly in response to stress. An alternative method of quantifying glucocorticoids is as hormone metabolites in faeces or urine giving a historical sample related to the gut passage time that is less sensitive to stressful events which cause spikes in the circulating hormone level. Although the concentration of glucocorticoid metabolites are influenced by faecal mass thereby potentially affecting any differences in hormone metabolites detected amongst samples. In the present study, we aimed to detect changes in levels of corticosterone, the primary bird glucocorticoid, in relation to the phase of reproduction, in a breeding population of collared flycatchers by sampling corticosterone metabolites in droppings. We also tested how corticosterone metabolite concentrations were affected by ambient temperature and related to body condition in adult birds. Our results indicate that the upregulation of corticosterone between incubation and nestling feeding in female birds is crucial for successful reproduction in this species. Also, females appear to down-regulate corticosterone during incubation in response to lower ambient temperature and poorer body condition. Our results did not indicate a relationship between dropping mass and corticosterone metabolite concentrations, which suggests that our findings were linked to the regulation of corticosterone in response to predictable and unpredictable challenges.