Neutral impact collision ion scattering spectroscopy (NICISS) is used to measure the energy loss in organic self-assembled monolayers (SAMs) on Au using Ne+ with low kinetic energies from 3 to 5 keV. With increasing film thickness, the energy loss of the projectiles increases because the projectile experiences more collisions with target atoms.Through comparing Monte-Carlo simulations with the NICISS experiments, it was found that contributions from nuclear stopping for Ne+ were significantly larger than for He+ mainly due to the stronger contribution of small-angle scattering of Ne+ making Ne NICISS unsuitable for depth profiling at energies of 5 keV or lower. The measured Ne+ electronic stopping in SAMs is small despite the large atomic number of Ne. Comparing experiments and DFT calculations shows that the latter accurately reproduce stopping powers for Ne+, while SRIM overestimates the stopping power. This contrasts He+ ions, where DFT and SRIM align closely with experiments.