The non-invasive nature of faecal glucocorticoid metabolite (FGM) assessment means that sample collection is on an opportunistic basis and samples cannot always be collected immediately upon defection during field studies. Faeces that have been exposed to heat and moisturemay not accurately reflect levels of FGM. Our study exposed male (n = 3) and female (n = 3) Grevy's zebra (Equus grevyi) faeces to six environmental conditions to simulate a range of weather and seasonal patterns (temperate climate, high heat, high heat and rainfall, temperate climate and rainfall, high heat/temperate climate and freeze/thaw) over a period of five days. FGMs were quantified using an enzyme linked immunoassay. Results showed that environmental conditions do impact upon FGM levels over time, particularly in conditions that include high heat; however, regardless of environmental exposure, metabolites remain similar to baseline levels for up to 8 h. We recommend that the investigation of environmental factors on sample integrity should be carried out as a validatory step when planning studies involving FGM analysis in any species.