Supply chain security encompasses measures preventing theft, smuggling, and sabotage through heightened awareness, enhanced visibility, and increased transparency. This necessitates the adoption of a security-by-design paradigm to achieve effective and efficient security measures, yielding additional benefits such as diminished supply chain costs. Given their vulnerability, transportation and logistics service providers play a pivotal role in supply chain security. This thesis leverages systems security engineering and security-by-design to provide a methodology for designing and evaluating security measures for physical transport goods. It formulates nine principles that define security-by-design and establishes a supply chain security framework. An adaptation of the TOGAF architecture development facilitates the creation of secure-by-design enterprise architectures. Security measures are documented using security-enhanced processes based on BPMN. This enables an analysis and compliance assessment to ascertain the alignment of security with business objectives and the adequate implementation of requirements. The culmination of these efforts is exemplified through a case study.