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• The SAFT-GT toolchain enables semi-automatic Attack-Fault Tree generation for enhanced safety and security assessment in self-adaptive systems. • The toolchain efficiently integrates into the feedback loop of self-adaptive systems, allowing for dynamic updates based on security assessments. • A user study with domain experts confirms the toolchain’s relevance and practical applicability in real-world scenarios. • Performance experiments demonstrate that the Attack-Fault Tree generation pipeline operates within feasible time constraints, supporting real-time applications. • The complete toolchain and resources are provided for download, fostering further research and collaboration in the field. In the rapidly evolving landscape of software engineering, the demand for robust and secure systems has become increasingly critical. This is especially true for self-adaptive systems due to their complexity and the dynamic environments in which they operate. To address this issue, we designed and developed the SAFT-GT toolchain that tackles the multifaceted challenges associated with ensuring both safety and security. This paper provides a comprehensive description of the toolchain’s architecture and functionalities, including the Attack-Fault Trees generation and model combination approaches. We emphasize the toolchain’s ability to integrate seamlessly with existing systems, allowing for enhanced safety and security analyses without requiring extensive modifications and domain knowledge. Our proposed approach can address evolving security threats, including both known vulnerabilities and emerging attack vectors that could compromise the system. As a use case for the toolchain, we integrate it into the feedback loop of self-adaptive systems. Finally, to validate the practical applicability of the toolchain, we conducted an extensive user study involving domain experts, whose insights and feedback underscore the toolchain’s relevance and usability in real-world scenarios. Our findings demonstrate the toolchain’s effectiveness in real-world applications while highlighting areas for future improvements. The toolchain and associated resources are available in an open-source repository to promote reproducibility and encourage further research in this field.