Secondary ion mass spectrometry (SIMS) relies on the fact that surface particles ejected from a solid surface are ionized under ion bombardment. By comparing the signal of molecular secondary ions desorbed from an organic film with that of the corresponding sputtered neutral precursor molecules, we investigate the variation of the molecular ionization probability when depth profiling through the film to the substrate interface. As a result, we find notable variations of the ionization probability both at the original surface and in the interface region, leading to a strong distortion of the measured SIMS depth profile. The experiments show that the effect can act in two ways, leading either to an apparent broadening or to an artificial sharpening of the observed film-substrate transition. As a consequence, we conclude that care must be taken when assessing interface location, width, or depth resolution from a molecular SIMS depth profile.