In the context of current state policy, focused on stable food security and achieving technological sovereignty, the systemic sustainable development of the agro-industrial sector becomes particularly important. Strategic priorities include increasing agricultural output, implementing import substitution measures through the use of domestically produced machinery and equipment, utilizing the national seed fund and breeding resources, and intensifying production using innovative technologies. These factors impose increased requirements on the efficiency of agricultural companies as the basic element of the sectoral structure. The methodological approaches proposed in the article for developing an organizational and economic mechanism to improve efficiency – in the context of enhancing strategic management of agricultural companies – aim to solve practical tasks of identifying and harnessing untapped opportunities to boost the business performance. Taking into account the priority objectives of developing agro-industrial production and the significant impact of state regulation measures on the economy of agricultural companies, the authors have classified state interests in the economic, social, and environmental spheres. The developed model of the organizational and economic mechanism is based on the need to align internal efficiency improvement objectives with national targets and sectoral development vectors. A key element in this mechanism is the assessment and monitoring block, which forms an information and analytical system to support the management of agribusiness development processes. A content analysis of existing scientific approaches to assessing the performance of economic entities has revealed the feasibility of applying an integral assessment based on a matrix (dynamic) model using non-parametric methods. The specifics of production processes in agriculture suggest two main stages: direct production of agricultural output and subsequent operations related to its primary processing, storage, and marketing. This division justifies the need for a management functional analysis and a separate assessment of the efficiency of an agricultural company’s production and commercial activities. The final assessment data will allow for scientifically substantiated identification of priority areas and the development of practical recommendations for improving the efficiency of business processes in agricultural companies.