This work proposes an Interconnection and Damping Assignment Passivity Based Control (IDA-PBC) to enhance power quality of an islanded Micro-grid (MG) including a photovoltaic main source (PV) and a Li-ion battery based Energy Storage System (ESS). In this MG, the PV generator-unit is controlled to provide its maximum power and the ESS-unit is controlled to ensure the desired voltage waveform at the Point of Common Coupling (PCC) and to support the PV source in order to satisfy the local loads. The IDA-PBC approach is chosen for its proprieties which allow the synthesis of asymptotically stable controllers for passive systems by the mean of the power system energy. In fact, the damping and interconnection coupling matrices of the IDA-PBC controller allows additional degree of freedoms in comparison to classical passivity controllers that enhance the convergence rapidity and the robustness under uncertainties. The mathematical model of the PV source and the Li-ion battery based ESS are presented. The power interface circuits are firstly represented through Park-coordinates then expressed in a Port-Controlled Hamiltonian (PCH) form. The obtained models are used to the design of the proposed IDA-PBC controller where the stability conditions are checked. The proposed control validity and performance are verified through comparison simulation tests with a conventional Proportional-Integral (PI) based control strategy. The obtained results show that the proposed control algorithm allows reducing the current and voltage overshoots under transient’s conditions in comparison to the PI controller. Furthermore, the proposed control achieves better voltage waveform at the PCC in steady state.