Organic production management fundamentals formation and implementation is the necessary condition for the economy at the sustainable development basis efficient functioning, providing high life quality and environmental public safety. Actual raises the need to manage the agricultural production ecological certification processes is driven by growing demand and incomplete satisfaction of the needs for organic certified products both in the domestic and foreign markets. The aim of the research is to justify recommendations related to Ukraine organic production organizational and management fundamentals through the national certification system for organic production creation and implementation improvement and development. The reasons of existing Ukraine organic production system is imperfect and its effective and efficient functioning in favor of national, the state and territorial communities’ interests indiscretion have been identified. Agricultural and food products certification institutional provision as the complex system of organizational, legal, economic and environmental regulation of social relations on the use of natural resources in the field of manufacturing processing and marketing of agricultural products has been determined. The significant role of accounting in the system of control over conformity by the operating rules of domestic organic products production have been determined.