Sake cake contains rice-derived components, as well as cell components and metabolites of Aspergillus oryzae and Saccharomyces cerevisiae. In this study, the effect of food processing on sake cake (sake-kasu) ingredients was investigated. Sake cake, obtained through brewing liquefied rice, was heat-dried (HD) or freeze-dried (FD) and analyzed. There were no differences in the amounts of proteins, lipids, carbohydrates, vitamin B6, choline, betaine, nicotinic acid, β-glucan and resistant proteins in HD and FD. There was also no difference in the amount of hydrolyzed amino acids in HD and FD, but many free amino acids were observed in HD. S-adenosyl methionine (SAM) was found to be abundant in FD. Meanwhile, nucleic acid-related components were found to be increased in HD, which seems to be due to the degradation of microbial metabolites. When considering the health benefits of sake cake, it is necessary to pay attention to the effects of processing method. Abbreviations CE-TOFMS: capillary electrophoresis time-of-flight mass spectrometry