The COVID-19 pandemic has highlighted that health security systems must be redesigned, in a way that they are better prepared and ready to cope with multiple and diverse health threats, from predictable and well-known epidemics to unexpected and challenging pandemics. A powerful way of accomplishing this goal is to focus the planning on health capabilities. This focus may enhance the ability to respond to and recover from health threats and emergencies, while helping to identify the level of resources required to maintain and build up those capabilities that are critical in ensuring the preparedness of health security systems. However, current attempts for defining and organizing health capabilities have some important limitations. First, such attempts were not designed to consider diverse scenarios and multiple health threats. Second, they provide a limited representation of capabilities and lack a systemic perspective. Third, they struggle to identify capability and resource gaps. In this article, we thus propose a new framework for identifying and structuring health capabilities and support health capability planning. The suggested framework has three main potential benefits. First, the framework may help policymakers in planning under high levels of uncertainty, by considering multiple realistic and stressful scenarios. Second, it can provide risk analysts with a more comprehensive representation of health capabilities and their complex relationships. Third, it can support planners in identifying resource and capability gaps. We illustrate the use of the framework in practice considering an outbreak scenario caused by three different health threats (COVID-19, Ebola, and Influenza viruses).