Introduction: Moringa peregrina (Forssk.) Fiori as a desert tree has economic, nutritional, and medicinal properties, and is constantly encountered with drought stress. In addition, the role of zinc oxide nanoparticles (ZnO-NPs) in regulating the drought stress which induces biochemical processes is uncertain in this plant. Therefore, this study aimed to investigate the biochemical alternations, namely, enzymatic and osmoprotectant which are induced by ZnO-NPs in ten populations of M. peregrina under drought stress. Materials and Methods: Moringa peregrina seeds were collected from southeast of Iran in 2014. The young plants were exposed to drought stress by withholding irrigation (until 50% filed capacity [FC]) 40 days after germination followed by spraying 0 (as control), 0.05, and 0.1% of the ZnO-NPs. Results: The alternations of Na/K ratio, enzymes activities, and osmoprotectant content varied under drought stress depending on the M. peregrina populations. Generally, drought stress significantly enhanced peroxidase (POD) and polyphenol oxidase (PPO) activities, as well as proline content in untreated plants. Further, the Na/K ratio and carbohydrates content significantly decreased under the drought stress. Furthermore, ZnO-NP treatment significantly enhanced POD and PPO activities, as well as proline and carbohydrates content under both well-watered (100% FC) and drought stress conditions (50% FC), and at the concentration of 0.05% rather than 0.1%, ZnO-NPs was more effective. Conclusion: Overall, ZnO-NP treatment could effectively improve the drought tolerance by enhancing the enzymes activities and osmoprotectant content in different M. peregrina populations under drought stress. Therefore, foliar application of ZnO-NPs at 0.05% concentration could be a recommended treatment for growing different M. peregrina populations under drought stress conditions.