Technical advances in automation, embedded hardware and virtualization nurtured the rapid development of safety-critical embedded systems. Avionic and Automotive are two of the domains that have seen significant development in recent years. However, the consideration of security of these embedded controllers often lags behind other functional improvements. This paper presents a brief threat landscape of embedded controllers and proposes a runtime security monitoring architecture aiming to protect these systems against threats that emerge during runtime. To facilitate rapid prototyping and encourage correct adaptation of security, similar to software development toolchains that guide development, the proposed architecture aims to provide a means for security monitoring that can be applicable to generic platforms.