Captive breeding is a vital conservation tool for many endangered species programs. It is often a last resort when wild animal population numbers drop to below critical minimums for natural reproduction. However, critical ecophysiological information of wild counterparts may not be well documented or understood, leading to years of minimal breeding successes. We collected endocrine and associated ecological data on a critically endangered ectotherm concurrently in the wild and in captivity over several years. We tracked plasma concentrations of steroid stress and reproductive hormones, body condition, activity, and environmental parameters in three populations (one wild and two geographically distinct captive) of ploughshare tortoise (Astrochelys yniphora). Hormone profiles along with environmental and behavioral data are presented and compared. We show that animals have particular seasonal environmental requirements that can affect annual reproduction, captivity affects reproductive state, and sociality may be required at certain times of the year for breeding to be successful. Our data suggest that changes in climatic conditions experienced by individuals, either due to decades-long shifts or hemispheric differences when translocated from their native range, can stifle breeding success for several years while the animals physiologically acclimatize. We also found that captivity affects stress (plasma corticosterone) and body condition of adults and juveniles differently and seasonally. Our results indicate that phenotypic plasticity in reproduction and behavior is related to environmental cues in long-lived ectotherms, and detailed ecophysiological data should be used when establishing and improving captive husbandry conditions for conservation breeding programs. Further, considering the recent revelation of this tortoises' possible extirpation from the wild, these data are critically opportune and may be key to the survival of this species.