<p>The global increase in natural disasters has profoundly impacted the spiritual health of those affected. Inadequate attention to this dimension of health during disaster recovery can lead to long-term adverse effects. This study aimed to evaluate the impact of a mosque-based spiritual rehabilitation intervention on the spiritual health of individuals affected by flooding. A randomized controlled field trial was conducted with 100 married men, aged 22–70&#xa0;years, in a rural community in Golestan, Iran. Participants were allocated into intervention and control groups through convenience sampling and simple randomization. The intervention consisted of six group sessions facilitated by the researcher, a village health worker, and the Imam of the village mosque in flood-affected areas. The spiritual health of the participants was assessed using a standardized questionnaire tailored for the Iranian context, administered before and after the intervention. The paired t-test showed a significant improvement in the spiritual health of the intervention group, with an increase of 24.9 units (<i>P</i> &lt; 0.001). Multivariate linear regression, adjusted for age and education level, confirmed a significant positive effect of the intervention on spiritual health scores among the flood-affected men (<i>β</i> = 28.3; <i>P</i> &lt; 0.001). These findings underscore the importance of integrating spiritual rehabilitation programs into all phases of disaster management. Such programs should be led by spiritual counselors with expertise in the religious beliefs and values of the affected community. In the preparedness phase, disaster managers and health policymakers should establish guidelines and provide necessary training to ensure the effective implementation of spiritual rehabilitation interventions.</p>