Quantification of glucocorticoid metabolites in feces has been shown to be a powerful tool in evaluating well-being in vertebrates. Little is known however about the hypothalamic–pituitary–adrenal axis response to stressors, and consequent glucocorticoid excretion, in reptiles. In a longitudinal study, fecal corticosterone metabolite (FCM) levels in green iguanas (Iguana iguana) were quantified during periods of rest and exposure to hypothesized stressors. FCM quantification was combined with behavioral analysis to further contextualize the measured increases. It was shown that both daily 5-minute handling/restraint, as well as housing devoid of climbing opportunity, resulted in increased FCM excretion. Behavioral analysis suggested that the iguanas were chronically stressed by the lack of climbing opportunity, whereas handling may have induced only a transient stress response. The experimental design, using repeated periods of stressor-exposure, also revealed a facilitating effect, where the two stressors potentiated one another. Furthermore, the order of the two stressors was found to be important. The study provides insight into the functioning of the hormonal stress response in green iguanas, and to the refining of their housing and handling.