This paper discusses the potential for photovoltaic systems to compensate the grid harmonics pollution by using the instantaneous power method. The objective is to develop an optimal algorithm of the control allowing both the active power transfer to the electrical grid and an optimal compensation of the harmonic pollution resulting from unbalanced non-linear loads as well as the compensation of the reactive energy involved. The studied system includes a photovoltaic generator (PV), a DC-DC converter that steps up the PV output to the DC link voltage level with maximum power point tracking (MPPT) control and an inverter that links the system to the grid with a variety of non-linear loads. This method consists in extracting the AC components of the active and reactive instantaneous powers which are related to the harmonics and to optimize the algorithm of the inverter control in order to compensate the disturbing currents caused by these powers. The study was realized according to different regimes that are related to both: the harmonic rate caused by the non-linear charges and the level of solar power received. The obtained results show the benefits of such optimization of the active filter compensation method, in order to improve the quality of the energy (THD ≤2.02%), while limiting the repercussions of the filter on the photovoltaic station and by automatically adapting to the variation of the solar irradiation and the unbalanced load without risk of resonance with the impedance of the grid that can be caused by the passives filters.