Development of microgrid systems (MGSs) due to restructuring has facilitated the installation of independently operated local energy resources (LERs) in power systems. In this new configuration, LERs would be operated by independent aggregators while the microgrid's control unit (MGCU) would coordinate the operational scheduling of aggregators. Independent aggregators of MGSs would strive to maximize their respective profits while delivering the flexibility operational service for addressing the operational issues in the system. Respectively, the unbalanced configuration of the MGSs due to unbalanced one-phase installation of LERs such as rooftop-photovoltaic units, demands, and storage units could be minimized by coordinated operation of aggregators. Consequently, this paper intends to develop a transactive-based methodology in order to enable the MGCU in an MGS to mitigate the unbalanced operation of the system caused by the unbalanced installation of LERs. In this context, MGCU would employ transactive control signals (TCSs) to alter the operational scheduling of aggregators connected to each phase of the power grid. This would enable mitigating the unbalance power flow in the system. Respectively, the unbalanced exchanged-power with the upper-level-system would be mitigated locally by each MGS, which improves the flexibility of the overall power system. Finally, the introduced methodology is conducted on an MGS with a multi-aggregator configuration to check out the advantages of the methodology in mitigating the unbalanced operational condition in the system.