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Security and privacy are among the main challenges in the systems of systems. The distributed ledger technology and self-sovereign identity pave the way to empower systems and users’ security and privacy. By utilizing both technologies, this paper proposes a distributed and self-sovereign-based framework for systems of systems to increase the security of such a system and maintain users’ privacy. We conducted an extensive security analysis of the proposed framework using a threat model based on the STRIDE framework, highlighting the mitigation provided by the proposed framework compared to the traditional SoS security. The analysis shows the feasibility of the proposed framework, affirming its capability to establish a secure and privacy-preserving identity management system for systems of systems.