Embedded Systems have become highly interconnected devices, being the key elements of the Internet of Things. Their main function is to capture, store, manipulate and access data of a sensitive nature. Moreover, being connected to Internet, expose them to all kind of attacks, which could cause serious consequences. Traditionally, during the design process, security, privacy and dependability (SPD) have been set aside, including them as an add-on feature. This paper provides a methodology together with a Multi-Metrics approach to evaluate the system SPD level during both the design and running processes. The simplicity, based on a single process during the whole system evaluation, and scalability, simple and complex systems are evaluated equally, are the main advantages. The applicability of the presented methodology is demonstrated by the evaluation of a smart vehicle use case.