Emergency planning in urban contexts should be based on preventative evaluation of potential impact with attention to the most vulnerable areas, multi-risk scenarios and the post-event performance of key infrastructures essential for emergency response operations. This approach is particularly relevant in cross-border areas, where coordinated preparedness and prevention efforts demand harmonized methodologies across different institutional frameworks, legal systems and infrastructural capacities. This paper proposes a practical and operational methodology for managing seismic, flood and combined risk in cross-border settings, which has been developed within BORIS2 (Cross Border Risk assessment for increased prevention and preparedness in Europe: way forward) project (UPCM-KAPP-PV- 2023 program). The proposed framework is structured in a four-step methodology that enables the complete assessment of scenario-based consequences at the affected urban environment and the corresponding performance of the Emergency Management System (EMS) at the municipal scale. The first step involves time-based risk assessment and intensity-based loss estimation to support risk-based decision-making and identifying geographical areas prone to significant damage or loss. A second step is focused on the selection of the most relevant scenarios including floods, earthquakes, and compound events all linked to a defined (mean) return period helping to understand the link between the severity of potential impacts and the likelihood of occurrence. Then, the event consequences are calculated according to the selected hazard scenario in terms of detailed estimates of residential building damage, injuries, displacement, and fatalities, as well as the evaluation of the expected damage of the essential facilities for emergency operations, including hospitals, fire stations, shelters, and coordination centres. The final step focuses on evaluating emergency response and management capabilities at the municipal level. By including critical infrastructure, such as the local road network, and simulating emergency response strategies the methodology provides an insight on the performance of the EMS under the considered scenario effectively supporting emergency preparedness.