Several management and control techniques for hybrid energy storage systems (HESS) with batteries and supercapacitors are presented in the literature applied to microgrids (MGs). The filter-based control strategy for defining the control loop actuation is one of the most widely used approaches with satisfactory performance. Variations of the Filter-Based Method (FBM) method are proposed to improve the control efficiency of the HESS under load disturbance and intermittent generator sources. However, not enough attention has been paid to the impacts of MG on the operational performance of batteries, despite the fact that they represent a non-negligible percentage of the total cost of MGs. In this paper, a control strategy called FBM-CSoC is proposed that focuses primarily on mitigating battery safety and degradation issues. The control strategy proposes a distribution of the charging and discharging current in a weighted proportional way to the normalized rated capacity and current state of charge (SoC) of each battery in the MG. This control strategy favors both the reduction of the internal temperature variation of the cells and the possibility of them operating in overcharging or over-discharging conditions. A comparative case study between the traditional FBM method and the FBM-CSoC, by means of numerical simulations, demonstrated that the load distribution occurs satisfactorily in energy storage systems. Finally, the FBM-CSoC method can be flexibly used for different types of battery technology and/or batteries with different SoCs integrated with supercapacitors.