AbstractUnderstanding how animals respond to stressors is critical for effective conservation. The present study aimed to evaluate the physiological recovery of the Shortnose Guitarfish, Zapteryx brevirostris after being incidentally captured by artisanal fleets and compared it to guitarfish with delayed mortality. Moreover, the study aimed to test the efficiency of a rehabilitation protocol for the species. To this end, individuals landed alive were transported to the rehabilitation facilities and kept in tanks under monitoring for 3 days. Physiological markers indicative of allostatic overload (i.e., lactate and phosphorus) and energy metabolism (i.e., glucose and β‐hydroxybutyrate) were assessed in the serum of the studied guitarfish: right after gillnet capture (i.e., post‐capture) and on rehabilitation (i.e., pre‐monitoring, post‐monitoring, as well as guitarfish that deceased during monitoring – post‐mortem). Results showed that the transportation and additional handling employed in the rehabilitation protocol did not increase the stress response, pointing to its potential efficacy in recovering debilitated, incidentally caught guitarfish before release. As for recovery success of monitored guitarfish, lactic acidosis was fully reverted after a 3‐day rest period, as was allostatic overload. The same was not observed in recovery failure. Correlation tests revealed key relationships between physiological markers, shedding light on how physiological pathways help guitarfish cope with capture and handling stress. This study highlights the valuable application of conservation physiology principles to fisheries management of this endemic and threatened guitarfish species.