Fourier transform infrared microspectroscopy using a synchrotron radiation source (SR-μFTIR) has great potential in the study of the ionizing radiation effects of human cells by analyzing the biochemical changes occurring in cell components. SR-μFTIR spectroscopy has been usefully employed in recent years in some seminal work devoted to shedding light on processes occurring in cells treated by hadron therapy, that is, radiotherapy with charged heavy particles (mainly protons and carbon ions), which is gaining popularity as a cancer treatment modality. These studies are particularly useful for increasing the effectiveness of radiotherapy cancer treatments with charged particles that can offer significant progress in the treatment of deep-seated and/or radioresistant tumors. In this paper, we present a concise revision of these studies together with the basic principles of μFTIR spectroscopy and a brief presentation of the main characteristics of infrared SR sources. From the analysis of the literature regarding the SR-μFTIR spectroscopy investigation on human cells exposed to proton beams, it is clearly shown that changes in DNA, protein, and lipid cell components are evident. In addition, this review points out that the potential offered by SR-μFTIR in investigating the effects induced by charged particle irradiation have not been completely explored. This is a crucial point for the continued improvement of hadron therapy strategies.