Context. 3C 279, the first quasar discovered to emit VHE γ-rays by the MAGIC telescope in 2006, was reobserved by MAGIC in January 2007 during a major optical flare and from December 2008 to April 2009 following an alert from the Fermi space telescope on an exceptionally high γ-ray state. Aims: The January 2007 observations resulted in a detection on January 16 with significance 5.4σ, corresponding to a F (>150 GeV) (3.8 ± 0.8) × 10-11 ph cm-2 s-1 while the overall data sample does not show significant signal. The December 2008-April 2009 observations did not detect the source. We study the multiwavelength behaviour of the source at the epochs of MAGIC observations, collecting quasi-simultaneous data at optical and X-ray frequencies and for 2009 also γ-ray data from Fermi. Methods: We study the light curves and spectral energy distribution of the source. The spectral energy distributions of three observing epochs (including the February 2006, which has been previously published) are modelled with one-zone inverse Compton models and the emission on January 16, 2007 also with two zone model and with a lepto-hadronic model. Results: We find that the VHE γ-ray emission detected in 2006 and 2007 challenges standard one-zone model, based on relativistic electrons in a jet scattering broad line region photons, while the other studied models fit the observed spectral energy distribution more satisfactorily.