Global climate change is negatively impacting global biodiversity and ectothermic vertebrates, with amphibians being the most imperiled vertebrate taxa. Increased mean global atmospheric temperatures, high rates of habitat degradation, and exposure to infectious diseases, such as chytridiomycosis, have contributed to population declines and extinctions of rare and endangered amphibian species. Field-based monitoring of physiological endocrine traits can help determine the sub-lethal effects of environmental stressors and provide early alerts when populations are chronically stressed. Recent advances in amphibian stress endocrinology include the development and use of non-invasive methods to quantify the glucocorticoid, or stress biomarker, corticosterone. Non-invasive methods, such as urinary, skin and buccal swabs, and water-borne hormone monitoring methods (suited for terrestrial and aquatic dwelling species), are available to quantify baseline and short-term physiological stress responses of amphibians under field settings. In this review, we illustrate, by using two case studies of aquatic and terrestrial amphibian species, the applications of non-invasive corticosterone monitoring methods to advance the ecological knowledge and conservation of imperiled amphibian species, discuss the limitations of these methods, and provide future directions for the use of non-invasive hormone monitoring methods. We highlight the use of non-invasive field endocrinology methods to monitor the impacts of environmental stressors on the physiology of amphibians, which can be applied to advance ecological research, conservation, and management of imperiled species.