The integration of a variety of heterogeneous energy sources and different energy storage systems has led to complex infrastructures and made apparent the urgent need for efficient energy control and management. This work presents a non-linear model predictive controller (NMPC) that aims to coordinate the operation of interconnected multi-node microgrids with energy storage capabilities. This control strategy creates a superstructure of a smart-grid consisting of distributed interconnected microgrids, and has the ability to distribute energy among a pool of energy storage means in an optimal way, formulating a virtual central energy storage platform. The goal of this work is the optimal exploitation of energy produced and stored in multi-node microgrids, and the reduction of auxiliary energy sources. A small-scale multi-node microgrid was used as a basis for the mathematical modelling and real data were used for the model validation. A number of operation scenarios under different weather conditions and load requests, demonstrates the ability of the NMPC to supervise the multi-node microgrid resulting to optimal energy management and reduction of the auxiliary power devices operation.