The direct effects of ionizing radiation on antibiotics are largely unknown. Here, we report mass spectra of the cationic products of the irradiation of three antibiotics by carbon ions at 10.4 MeV kinetic energy. Carbon ion beams used in cancer treatments have this energy when they deliver the maximum dose to malignant cells. We find that upon single carbon ion collision, extensive fragmentation of antibiotics occurs, predominantly through channels similar to those observed in soft X-ray photoabsorption. However, new product ions are also detected and attributed to the ability of MeV carbon ions to eject electrons from the molecular target in an unspecific manner. Proton transfer appears to play a key role in the dissociation dynamics of rifamycin and actinomycin, and it is complemented by sodium transfer in sodiated rifamycin and its dimer. Importantly, we report the first evidence for abundant loss of H from precursor ions, as well as for intramolecular cross-linking triggered by carbon ion collision. All these processes most probably take place in the vibrationally hot electronic ground state of the molecular system.