Context : Polarization of maser emission contains unique information on the magnetic field in the densest regions of massive star formation . Aims : Recently , the magnetic field induced Zeeman splitting was measured for the strongest known 6.7 GHz methanol maser , which arises in the massive star forming region G09.62+0.20 . This maser is one of a handful of periodically flaring methanol masers . Magnetic field measurements can possibly provide insights into the elusive mechanism responsible for this periodicity . Methods : The 100-m Effelsberg telescope was used to monitor the 6.7 GHz methanol masers of G09.62+0.20 , in weekly intervals , for just over a two month period during which one of the maser flares occurred . Results : With the exception of a two week period during the peak of the maser flare , we measure a constant magnetic field of B _ { || } \approx 11 \pm 2 mG in the two strongest maser components of G09.62+0.20 that are separated by over 200 AU . In the two week period that coincides exactly with the peak of the maser flare of the strongest maser feature , we measure a sharp decrease and possible reversal of the Zeeman splitting . Conclusions : While the two phenomena are clearly related , the Zeeman splitting decrease only occurs near the flare maximum . Intrinsic magnetic field variability is thus unlikely to be the reason for the maser variability . The exact cause of both variabilities is still unclear , but it could be related to either background amplification of polarized emission or the presence of a massive protostar with a close-by companion . However , the variability of the splitting between the right- and left-circular polarizations could also be caused by non-Zeeman effects related to the radiative transfer of polarized maser emission . In that case we can put limits on the magnetic field orientation and the maser saturation level .