A socio-technical system of systems (SoS) is a collaboration of independently operated and managed systems. These constituent systems join the SoS to work together for a common goal: to achieve positive emergent behaviors such as greater capability, efficiency, resource utilization, reliability, and robustness. To achieve such a goal, an SoS needs to be well-managed with mitigation plans for all system risks. However, existing risk management strategies were developed for individual, non-integrated systems and are therefore inadequate for use with SoS. This paper uses the COVID-19 pandemic in Sweden as a case study for exploring risk analysis for SoS management. We performed a risk analysis of this SoS based on STAMP (System-Theoretical Accident Model and Processes), an existing method from the safety domain, as part of developing a preliminary risk analysis process for practitioners. Preliminary results reveal that extended SoS structures, uncertainty-driven decision-making, emerging behavior, and changes in trust, policy, and legislation pose significant challenges. The study’s contribution is that our findings provide a knowledge base to act as a guide for risk management of SoS. Applying a method for safety analysis to crisis management also extends the body of knowledge on methods for SoS risk analysis.