The article discusses the issues of development and analysis of diagnostic procedures for business processes during enterprise management. The digitalization has become a priority at the state level of every country, influencing the daily lives of citizens and the enterprises activity. As a result, the ability to gather, analyze, process, and use the data has taken center place to support effective decision-making and sustain competitive market positions. The article considers the factors influencing the choice of data processing tools, analyses the difficulties faced during the data processing methods implementation, and outlines the essential features of such systems for effective management of enterprise activity. The main attention was paid to the development of a data processing method during the state diagnosis of business processes in case of assessing their compliance. The method involves calculating the probability density function for the costs of restoring the normal functioning of business processes and statistical characteristics of the probability of correct decision-making. Additionally, the article includes numerical examples demonstrating the use of this method to the business processes of an aviation enterprise engaged in providing and performing technological procedures for the operation of aircraft. The proposed data processing model can be used to analyze the efficiency of enterprises’ business processes and make decisions on organizational structure optimization to minimize the costs spent by enterprise.