Ion beam analysis (IBA) is an established method to determine the concentration and the distribution of elements in art and archaeological objects. However, especially for organic specimens, caution must be taken to avoid harmful effects. In this work, the possible modification of recent calf parchment samples by proton beam irradiation was investigated applying fluences (given as deposited charge per unit area) both within and beyond the usual analytical practice. Attenuated Total Reflection Fourier Transform Infra-red Spectroscopy (FTIR-ATR) and Optical Coherence Tomography (OCT) were employed to assess changes, inspected from the surface of the samples. Although both techniques are apt to detect alterations of parchment in general, in the case of particles, which deposit the majority of their energy below the surface these techniques could not detect changes at low fluences. However, a simple “bath test” (short immersion in liquid) proved that disintegration within the material had already happened. After the “bath test”, OCT and digital 3D microscopy were used to check the discontinuities in the material, especially for low fluences when the visual inspection might have missed them. Unfortunately, simply monitoring organic objects such as parchment during or after ion beam irradiation, non-destructively, is not sufficient to claim absolute harmlessness, as some studies in the past did. In line with our former findings using electron microscopy on cross sections, we found that 2.3 MeV protons with a deposited charge of 0.5 µC/cm2 caused no changes affecting the integrity of parchment but 2 µC/cm2 apparently did under the applied experimental conditions. To ensure the required analytical signal at a relatively low deposited charge, the detection system must be optimized for efficiency. Nevertheless, since the variability of the historic materials and the measurement set-ups are considerable, these values cannot be taken as absolutes, but only as guides, both for further IBA studies and for studies conducted in the past.