Radiotherapy is one of the most common approaches for cancer treatment, especially in the case of peripheral nervous system tumors. As it requires exposure to high doses of ionizing radiation, it is important to look for substances that support efficient reduction of the tumor volume with simultaneous prevention of the surrounding noncancerous cells. Cannabidiol (CBD), which exhibits both anticancer and neuroprotective properties, was applied as a potential modulator of radiological response; however, its influence on cells undergoing irradiation remains elusive. Here, we have applied high-resolution optical spectroscopy techniques to capture biomolecules associated with CBD shielding of normal and damaging cancerous cells upon X-ray exposure. Conventional Raman (RS) and Fourier transformed infrared (FT-IR) spectroscopies provided semiquantitative information mainly about changes in the concentration of total lipids, DNA, cholesteryl esters, and phospholipids in cells. A through assessment of the single cells by atomic force microscopy coupled with infrared spectroscopy (AFM-IR) allowed us to determine not only the alterations in DNA content but also in its conformation due to cell treatment. Pronounced nanoscale changes in cholesteryl ester metabolites, associated with CBD treatment and radiation, were also observed. AFM-IR chemoselective maps of the single cells indicate the modified distribution of cholesteryl esters with 40 nm spatial resolution. Based on the obtained results, we propose a label-free and fast analytical method engaging optical spectroscopy to assess the mechanism of normal and cancerous cell susceptibility to ionizing radiation when pretreated with CBD.