Ensuring the financial security of agro-industrial enterprises is crucial for the sustainable development of the sector and the achievement of national goals. The four-stage methodological approach presented in this article for assessing the financial security of agro-industrial enterprises enables timely risk diagnosis and the development of effective mechanisms to mitigate internal and external threats, thereby protecting companies’ financial interests. The first stage, identifying vulnerabilities in the company’s financial security system, proposes key parameters for a rapid financial assessment and a bankruptcy prediction model. The conducted analysis and assessment of of the food industry enterprise’s financial condition revealed discrepancies in the results. Therefore, the second stage incorporates factors that consider investment and tax aspects in addition to financial metrics. Based on an analysis of various methodologies, an indicator method was selected, and an integral criterion, incorporating 15 specific measures, was developed to assess financial security. The number of indicators can be adjusted based on the specific conditions and goals of each enterprise. The integral indicator’s scale identifies three levels of security: low, medium, and high. To ensure high financial security and timely response to threats, the third stage recommends prioritizing significant risks using risk maps, spirals, and a bow-tie model. The results of the risk analysis will inform evidence-based measures to manage and minimize financial security risks.