Harmonic disturbance is an issue that can be solved using active filters connected at the point of common coupling (PCC). Power inverter based distributed generation systems (DGs) can operate as active filters as well as supplying power to the grid. Several works perform the total harmonic compensation at the PCC, which is in general not economically attractive considering that there are regulatory standards that establish the allowed limits of distortion. This paper proposes the use of a resonant proportional controller (PR) strategy for three-phase current-controlled voltage source inverters, present in microgrids to control the injected power into the grid and compensate partial harmonic components of current at the PCC. The compensation strategy is performed by adding proportional plus integral (PI) controllers to adjust the amplitude of the currents according to adopted harmonic distortion references. Scenarios with total and partial harmonic distortions compensation at the PCC were analyzed and the results showed that the use of the partial compensation strategy allowed a 10% increase in the value of the fundamental current in relation to the total compensation strategy.