Energy storage systems (ESSs) bring various opportunities for a more reliable and flexible operation of microgrids (MGs). Among them, energy arbitrage and ancillary services are the most investigated application of ESSs. Furthermore, it has been shown that some other services could also be provided by ESSs such as power quality (PQ) improvements. This issue could be more challenging in MGs with widespread nonlinear loads injecting harmonic currents to the MG. In this paper, the feasibility of ESSs to act as coordinated active harmonic filters (AHF) for distributed compensation was investigated. An optimization model was proposed for the coordination of the harmonic compensation activities of ESSs. The model takes into account the various technical and systematic constraints to economically determine the required reference currents of various AHFs. Simulation cases showed the performance of the proposed model for enhancing the harmonic filtering capability of the MG, reduction in the compensation cost, and more flexibility of the distributed harmonic compensation schemes. It was also shown that ESS activities in harmonic compensation do not have much of an effect on the ESSs revenue from energy arbitrage. Hence, it could make ESSs more justifiable for use in MGs.