A non-linear control structure for a Photovoltaic (PV), battery and supercapacitor based stand-alone DC-microgrid is presented in this paper. Most of the conventional PI-based linear control structures reported in the literature have been designed around a single operating point and also supercapacitor voltage has not been regulated. Though supercapacitor voltage is regulated in some of the works, a dedicated controller has been used which increases controller count and makes designing/tuning of controllers together for desired system performance complicated. However, due to self-discharge or frequent discharge during operation, supercapacitor voltage can reach the lowest value which affects controller performance and even makes the system unstable. So, a robust non-linear controller: Interconnection Damping Assessment-Passivity Based Controller (IDA-PBC) is implemented as an outer loop controller to regulate DC-link and supercapacitor voltages. Also, a Finite Control Set-Model Predictive Control (FCS-MPC) which is intuitive in nature is implemented as inner current controllers. The proposed control structure is digital-friendly and can address the limitations of linear PI-control structure such as (i) Controller conflicts in designing the multiple controllers, (ii) Small region of stability (iii) Supercapacitor voltage regulation. Finally, the proposed control structure is verified through simulation and experimental results.