We investigate the causes of energetic proton (80–540 keV) depletions measured during the two most distant flybys of Europa by Galileo, E17 and E25A, which encountered the Alfvén wings. First, by simulating the proton flux with a Monte Carlo particle tracing code we investigate the effect of: electromagnetic field perturbations, the induced dipole, atmospheric charge exchange and plumes. Inhomogeneous fields associated with the Alfvén wings and the ionosphere strongly affect the depletions. For homogeneous fields the depletion along the trajectory is focused on a narrow pitch angle range and has no structure, whereas the depletion for perturbed (inhomogeneous) fields represents a wider and complex structure. Furthermore, also the induced dipole alters the depletion structure. The effect of plumes (density 2.5 × 1015 m−3) and charge exchange on the proton depletion is minor. Second, we compare the simulations to the proton measurements. The simulations with inhomogeneous fields describe the data qualitatively better than the homogeneous case, suggesting that indeed field perturbations are responsible for the measured losses. We attribute discrepancies between the simulations and the proton measurements to discrepancies between the simulated and real fields. We argue that simulating the fields along the trajectory is a good first step, but that ideally the energetic ion flux is reconstructed well to gain confidence in the interpretation of the simulated magnetic field. In conclusion, energetic ion observations along distant flybys through the Alfvén wings are suitable for isolating the characteristics of the global configuration of the magnetospheric interaction region of Europa (or other moons).