The Flat Spectrum Radio Quasar 3C 279 has been very active since a few years with multiple flaring events occurring at high energies. As part of the H.E.S.S. Target of Opportunity program, 3C 279 was observed multiple times in 2017 and 2018 following high states in optical (February and March 2017) or at high energies as seen with Fermi-LAT (June 2017, January, February and June 2018). While in January 2018 H.E.S.S. detected an unexpected very high energy (VHE) flare at the end of the MeV-GeV flaring state, in June 2018 it was possible to follow almost continuously the decaying part of a strong Fermi-LAT flare, observing with the full array for several nights after the peak of the GeV gamma-ray emission. This has lead to the detection of the source with very high significance. We present here the temporal and spectral results of the H.E.S.S. II dataset together with an overview of the strong multi-wavelength activity seen from 3C 279 between 2017 and 2018.