Horses are susceptible to developing large areas of pulmonary atelectasis during recumbency and anesthesia. The subsequent pulmonary shunt is responsible for significant impairment of oxygenation. Since ventilation perfusion mismatch persists into the post-operative period, hypoxemia remains an important concern in the recovery stall. This case report describes the diagnosis and supportive therapy of persistent hypoxemia in a 914 kg draft horse after isoflurane anesthesia. It highlights how challenging it can be to deal with hypoxemia after disconnection from the anesthesia machine and how life-threatening it can become if refractory to treatment. Furthermore, it stresses the point on the interactions between hypoxemia and other factors, such as residual drug effects and hypothermia, that should also be considered in the case of delayed recovery from general anesthesia.