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Strong depletions of energetic protons (115‐244 keV) were observed during Galileo flyby E26 of Europa. We simulate the flux of energetic protons using a Monte Carlo particle backtracing code and show that energetic proton depletions during E26 are reproduced by taking into account the perturbations of the electromagnetic fields calculated by magnetohydrodynamic (MHD) simulations and charge exchange with a global atmosphere and plume. A depletion feature occurring shortly after closest approach is driven by plume associated charge exchange, or a combination with plume associated field perturbations. We therefore conclude, with a new method and independent dataset, that Galileo could have encountered a plume during E26.