Agri-food complex of the Republic of Belarus and its regional entities are at the stage when transition to new quality of economic growth based on forming sustainable competitive potential of industries and enterprises, maximum use of reserves of performance and efficiency growth, innovation and investment activities activation taking into account world market trends, is of particular relevance. In this regard, it is required to analyze the stability of regional agri-food complexes based on methodology considering their features, identify the enabling factors and conditions, assess the impact of negative trends and propose ways to improve regulatory mechanisms. The paper presents the results of research of methodological and practical aspects of ensuring sustainable development of agri-food complex. Criteria, evaluation indicators, principles and basic regulatory mechanisms were developed. Based on a special methodology for arranging a system of partial and integral criteria, the stability of agri-food complex functioning in the regions of Belarus was assessed, the main factors according to effect line were identified and classified. Methodological recommendations for assessing sustainability of agricultural production at the level of districts and organizations have been developed and tested on the example of Vitebsk region, they contain groups of indicators and algorithm that allows ranking objects according to potential for sustainability and achieved production and economic results, as well as applying differentiated approaches for state regulation. A functional model for controlling sustainable development of the regional agri-food complex is presented, including target, regulatory and regulated subsystems, based on pervasive arrangement and integration of control functions and tasks.