In this paper, the power quality of interconnected microgrids is managed using a Model Predictive Control (MPC) methodology which manipulates the power converters of the microgrids in order to achieve the requirements. The control algorithm is developed for the microgrids working modes: grid-connected, islanded and interconnected. The results and simulations are also applied to the transition between the different working modes. In order to show the potential of the control algorithm, a comparison study is carried out with classical Proportional-Integral Pulse Width Modulation (PI-PWM) based controllers. The proposed control algorithm not only improves the transient response in comparison with classical methods but also shows an optimal behavior in all the working modes, minimizing the harmonics content in current and voltage even with the presence of non-balanced and non-harmonic-free three-phase voltage and current systems