In today's interconnected digital ecosystem, protecting cyber‐physical systems is critical. STPA‐Sec is a systematic method that allows to analyze system designs and identify vulnerabilities in those designs from the onset and throughout the system lifecycle. In this article, we describe a carefully designed metamodel that accommodates the concepts and steps of the method. We translate key concepts from STPA‐Sec into a metamodel, with the intention of facilitating a more structured and disciplined application of STPA‐Sec. We demonstrate the advantage of using the metamodel in two case studies. This article offers a step forward in the rigorous application of STPA‐Sec.