“Security by design” is the term for shifting cybersecurity considerations from a system’s end users to its engineers. To reduce the end users’ workload for addressing security during the systems operation phase, security decisions need to be made during engineering, and in a way that is traceable for third parties. However, engineers of cyber-physical systems (CPSs) or, more specifically, industrial control systems (ICSs) typically neither have the security expertise nor time for security engineering. The security-by-design decisions method presented in this work aims to enable them to identify, make, and substantiate security decisions autonomously. Core features of the method are a set of function-based diagrams as well as libraries of typical functions and their security parameters. The method, implemented as a software demonstrator, is validated in a case study with the specialist for safety-related automation solutions HIMA, and the results show that the method enables engineers to identify and make security decisions they may not have made (consciously) otherwise, and quickly and with little security expertise. The method is also well suited to make security-decision-making knowledge available to less experienced engineers. This means that with the security-by-design decisions method, more people can contribute to a CPS’s security by design in less time.