Islanded microgrids face difficulties due to the presence of nonlinearity, asynchronous load, and unknown load dynamics. Moreover, conventional control schemes in the islanded microgrids show slow dynamic response, significant voltage-current oscillations, frequency change, low output power quality, and less reference tracking capability. In this regard, a robust and high performance controller is required against the instability issues related to various load conditions and sudden load changes in the solar photovoltaic (PV)-based solar photovoltaic (PV) based islanded microgrids. This paper presents the design and implementation of a second-order high performance resonant controller for robustness and improving the stability of a solar PV based three-phase islanded microgrid (TPMG) under varying system conditions. The design of the proposed controller is based on a backstepping scheme where control Lyapunov functions are used to find transfer functions. The transfer functions that are obtained by this approach are the transfer functions of a resonant controller with proportional-integral controllers. The performance of the proposed controller is investigated in MATLAB/Simulink. The simulation results demonstrate the robustness of the proposed controller in terms of stability, dynamic responses, voltage-current oscillations, total harmonic distortion, and reference tracking of the TPMG. Moreover, the performance of the proposed controller is illustrated against various load dynamics and sudden load changes. A laboratory-scale experiment verifies the simulation results of the proposed controller.