The basis of this research consists of conceptual developments of a methodological nature that allow one to diagnose and assess the limitations, threats and challenges of an economic, social, environmental, resource-technical, administrative and legal nature across the vertical of the economic levels of an integral national system. The purpose of the paper is to formulate an original methodological approach to the research of economic security, considering the causal connection between the elements of the totality of individual determinants and conditions characterizing threats and challenges. The peculiarity of the proposed approach lies in the fact that the authors consider the enterprise as the initial level of the economic system. The economic security of an enterprise largely determines the economic security of other levels of this system. They represent the business environment that can be a carrier of external threats that negatively affect the economic security of the enterprise. We believe that without ensuring economic security at all levels of the economic hierarchy, it is impossible to ensure the implementation of the concept of sustainable development. The use of the matrix principle justifiably allows the authors to solve the evaluation problem within a single methodological approach. It allows identifying the determinants that most affect economic security. It is assumed that the diagnostic results will allow developing specific measures to eliminate or reduce the role of negative factors and motivational and stimulating measures that ensure the resolution of contradictions arising from the presence of restrictions, including environmental and social, on entrepreneurial activity.