The article deals with the problems of increasing the bio-productivity of agroecosystems with the help of intelligent decision-making procedures to optimize the management of their state. In the course of research, the author developed an algorithm for the interaction of operational and planned. Management of the state of the agroecosystem, characterized in that the values of the controlled parameters change due to changes in the initial formulation of the optimization problem and the actual content of humus at the beginning of rotation. This allows you to manage the state of the agroecosystem, taking into account the need to restore humus. In addition, the author proposes a method and algorithm for decision support system for managing the state of the agroecosystem, which allows to rationalize the process of fertilization, to ensure an increase in crop yields, profitability of agricultural production and preservation of soil fertility. With the help of decision support system (DSS), the conditions for preserving soil fertility (variants of applied mineral and organic fertilizers that stabilize humus) were determined and forecasts of bio-productivity and economic efficiency.