One of Oman's most cultivated fruit crops, lime, is suffering severely from a devastating disease called witches’ broom. Climatic conditions of the growing regions further aggravate the presence, severity and spread of the deleterious disease. Huge efforts have been made by both farmers and the government to alleviate the economic impact of the disease infection and improve the net benefit from lime production. Pruning of the symptomatic branches is considered an effective method of controlling Witches’ Broom Disease of Lime (WBDL). This study develops a dynamic bioeconomic model using the Bellman equation to derive the optimal management strategy for WBDL and the optimal replanting age of citrus trees after the first attack under multiple scenarios of disease management options and climate conditions. In addition, the study investigates different scenarios of disease presence and spread given different climatic conditions of arid, semi-arid and tropical zones in Oman. The first novelty of the study is that it is the first to model and address the economic loss associated with the disease risk or economic gain resulting from disease management. Moreover, it is the first to incorporate climate conditions into bioeconomic modeling for managing agricultural diseases or evaluate the effects of climate change and the interaction with WBDL using a bioeconomic model. To the best of our knowledge, the study is the first attempt to provide a detailed and thorough economic analysis of possible climatic factors that may influence the presence and spread of the WBDL. In addition, the utilized function that describes the total damage caused by the disease is created by incorporating the disease's behavior in the field and the characteristics of the fruit. This study is among the few that employ a dynamic bioeconomic model and analyze agricultural resources under risk in Arabian countries. The study aims to help citrus growers make the best disease-mitigating decisions and policymakers in planning and implementing effective treatment programs for the alignment of both farmer and government interests of profit maximization and social value. The results of the study show that the farmer’s disease treatment decisions are significantly influenced by the disease density and insect vector level on the farm, and adverse climate conditions have a significant negative impact on the economic value of citrus cultivation. Overall, the net benefit in the arid region is significantly lower than that of the other two zones for all the considered scenarios. There is a 55.6% increment to the expected farm value due to the disease management in the arid zone, while the increments are relatively lower in the semi-arid and tropical zones, 33.5% and 36.5%, respectively. Introducing climatic factorsinto the model further increases the benefit of implementing management action. While the increment is nearly 100% for the arid zone, the value in semi-arid and tropical zones increase by 68.2% and 72.6%, respectively. There is a massive reduction in farm value, 29%, due to climate conditions in arid zones if the disease is left unmanaged (from 20,813 OMR to 14,774 OMR). However, management of the disease has led to an improvement in farm value by 8.8% (from 29,538 OMR to 32,375 OMR). The adverse effect of climate conditions on the expected net benefits is almost the same for semi-arid and tropical zones, 24.5% and 4.8%, and 24.1% and 3.4%, for the considered scenarios. A similar pattern is observed in the optimal replanting age, with the arid zone having the earliest replanting age of 11 years in the absence of climate conditions. The rotation age further decreases to 9 years in the presence of severe climate conditions. Hence, it is optimal for citrus growers to consider WBDL treatment and climate conditions before any management decision for better outcomes. The result further indicates that farmers should undertake an increasing level and frequency of disease treatment to maximize the net benefit from lime cultivation as opposed to the current management practice. It is recommended that the government raise awareness of the cost-sharing strategy among neighboring farmers as a sort of cost-efficient collaborative effort to relieve it of the financial burden. Furthermore, large-scale lime production should be done in the middle or southern region to avoid the high risk of disease and climate in the northern region, thus maximizing profits. The findings of this study imply that the government (regulator and subsidy provider) as well as citrus growers should realize the importance of a well-managed and effective disease control program and the consequences of such a program on increasing the production of citrus.