The digitalization and smartization of modern digital systems include the implementation and integration of emerging innovative technologies, such as Artificial Intelligence. By incorporating new technologies, the surface attack of the system also expands, and specialized cybersecurity mechanisms and tools are required to counter the potential new threats. This paper introduces a holistic security risk assessment methodology that aims to assist Artificial Intelligence system stakeholders guarantee the correct design and implementation of technical robustness in Artificial Intelligence systems. The methodology is designed to facilitate the automation of the security risk assessment of Artificial Intelligence components together with the rest of the system components. Supporting the methodology, the solution to the automation of Artificial Intelligence risk assessment is also proposed. Both the methodology and the tool will be validated when assessing and treating risks on Artificial Intelligence-based cybersecurity solutions integrated in modern digital industrial systems that leverage emerging technologies such as cloud continuum including Software-defined networking (SDN).