Urban areas in Java are increasingly affected by flood disasters due to rapid urbanization and climate change, leading to significant socio-economic and safety challenges. This study investigates innovative mosque architectural designs that not only serve religious functions but also operate as effective evacuation shelters during flood events. Utilizing a qualitative research methodology, including comprehensive literature reviews and case study analyses of Masjid Raya KH. Hasyim Asyari and Masjid Jami’ Baitul Mannan, the research identifies critical design elements that enhance safety and resilience. Key findings indicate that elevated foundations, flood-resistant materials, spacious open areas, and clearly delineated evacuation routes are essential components of adaptive mosque design. Moreover, the integration of modern technologies, such as real-time flood monitoring and early warning systems, further enhances the effectiveness of these structures as emergency shelters. The dual role of mosques as centers of spiritual and social support positions them uniquely to contribute to disaster management frameworks. This study offers practical design recommendations and policy insights, advocating for an interdisciplinary approach to urban planning that prioritizes both cultural heritage and disaster resilience. By redefining mosque design, the research aims to strengthen community preparedness and mitigate the adverse impacts of flooding in urban Java with utmost urgency.