In this work, we have investigated the influence of the magnetic field configuration during magnetron sputtering of WO3 in order to establish the ion flux-film structure relationship. An asymmetric bipolar pulsed DC magnetron sputtering (PDMS) was used with two magnetic field configurations: balanced (BM) and unbalanced (UMB) magnetic configurations. Ion Energy Distribution Functions (IEDFs) of the main ion populations (Ar+, O+) were recorded. The IEDFs are broad with, in addition of the thermalized distribution around 2 eV, two peaks with available ion kinetic energy up to 40–100 eV associated with the positive part of the pulse. Comparing the BM and UBM data, we calculated an increase by a factor of 5 of the ionic current while the average energy per ion was kept constant (~44 eV). X-ray diffraction demonstrates the influence of the magnetic configuration on the coating phase constitution. The films are crystallized in the WO3 monoclinic phase with preferential orientations along the c axis using the BM configuration and along the a axis using the UBM one’s. On the other hand, it has been demonstrated that the grain size increases with the thickness using the BM configuration (up to 18 nm) while it remains constant using the UBM one’s (~7 nm).