Greenhouses are implemented all over the world to increase agricultural production thanks to contolled environmental conditions (inside temperature, moisture and CO2 contents). However, such systems are energy-intensive. The presented work focuses on controlling a greenhouse' onsite multi-energy system (gas, heat and electricity), extended to a multi-flow system as the CO2 produced by the energy units is used as a plant fertilizers. In this view, a three levels hierarchical control has been developed: a steady state economic MPC is combined with a dynamic Multienergy MPC and low-level PID controllers. This new controller aims at determining the best synergies for economic flows management, subject to compliance with the required climatic conditions in the greenhouse. The proposed controller is applied to a greenhouse which energy system is based on a thermal energy storage fuelled by a gas boiler and a combined heat and power unit. The results are confronted to a usual ruled-based controller performed by greenhouses owners, showing a more efficient dynamic functioning of the energy system. Consequently, less gas is consumed (80.79 t to 76.03 t), heat is produced when needed, and electricity from the CHP is economically optimized allowing less importation from the grid (from 17.80 MWh to 15.88 MWh), and profitable selling.