For decades, traditional mutation breeding technologies using spontaneous mutation, chemicals, or conventional radiation sources have contributed greatly to the improvement of crops and microorganisms of agricultural and industrial importance. However, new mutagens that can generate more diverse mutation spectra with minimal damage to the original organism are always in need. In this regard, ion beam irradiation, including proton-, helium-, and heavier-charged particle irradiation, is considered to be superior to traditional radiation mutagenesis. In particular, it has been suggested that ion beams predominantly produce strand breaks that often lead to mutations, which is not a situation frequently observed in mutagenesis induced by gamma-ray exposure. In this review, we briefly describe the general principles and history of particle accelerators, and then introduce their successful application in ion beam technology for the improvement of crops and microbes. In particular, a 100-MeV proton beam accelerator currently under construction by the Proton Engineering Frontier Project (PEFP) is discussed. The PEFP accelerator will hopefully prompt the utilization of ion beam technology for strain improvement, as well as for use in nuclear physics, medical science, biology, space technology, radiation technology and basic sciences.