Jupiter’s largest moon Ganymede has its own intrinsic magnetic field, which forms a magnetosphere that is embedded within Jupiter’s corotating magnetospheric plasma. This scenario has been shown to lead to complex ion precipitation patterns that have been connected to heterogeneous space weathering across Ganymede’s surface. We present the first simulations of energetic neutral atoms (ENAs) from backscattered H, O, and S ions, accounting for magnetospheric plasma precipitation and Ganymede’s heterogeneous surface composition. Our model shows that backscattering introduces significant atomic H and O populations to Ganymede’s ENA environment, which will allow remote observation of ion–surface interactions at Ganymede. There are distinct differences between H ENA emissions at Ganymede and the Moon, with orders of magnitude lower fluxes below 1 keV but a significant tail above 1 keV. Backscattered H ENAs will also dominate over sputtered H contributions above energies of around 1 keV, while O ENAs are less likely to be distinguished from sputtered ENAs. The backscattered H ENAs thus represent a promising candidate for studying the plasma–surface interaction on Ganymede with future observations of ESA’s JUICE mission.