The research provides a comparative analysis of the activities of small and medium-sized enterprises producing dual-use products for 2022–2024 based on the reporting documents on the activities of entrepreneurs in the Nizhny Novgorod Region. It is characterized by significant shortcomings in managing business processes and increased output volumes for enterprises in the region. Based on the research findings, the authors present the development of an innovative approach to optimizing the organizational structure of a small and medium-sized enterprise using the example of one of its leading divisions—the technical control department. The proposed classification method centers on a matrix model developed in this study. It applies the non‑negative Tonimoto‑Rogers criterion to gauge the similarity between pairs of functions, using dichotomous partitioning followed by pairwise comparison. The optimal organizational structure obtained by an algorithm in digital format does not duplicate functions and information loops, which increases production efficiency by reducing production costs.