In this paper, to address the problem of multiple actuator faults in autonomous AC microgrids, a cooperative fault-tolerant control (CFTC) algorithm is designed. The proposed algorithm is responsible for the potential heterogeneous faults in units’ actuators, like loss of effectiveness (LOE) and unknown bias faults. Furthermore, the communication network is considered as a directed switching graph, which can be viewed as an unreliable network and makes the CFTC problem more challenging. Also, in addition to the distributed generation (DG) units, we consider the presence of distributed energy storage (DES) systems that operate in the islanded microgrid. In addition to the voltage and frequency regulation, it is required to balance the state of charge (SoC) of DESs to achieve accurate active power-sharing. Finally, to evaluate the performance of the proposed CFTC algorithm, simulation studies are carried out on a test microgrid system in MATLAB/Simulink environment, and the results are compared with several previously-reported methods. Simulation results and comparison with other previously-reported techniques reveal the effectiveness and accuracy of the proposed method in regulating microgrid voltage and frequency, balancing of SoC, and providing accurate proportional active power-sharing.