SummaryFermentation of yellow maize using different inocula yields mahewu products with varying compositions. Comprehensive analysis of the metabolites influencing distinctive characteristics of mahewu from sorghum malt (YMSM); wheat (YMW), malted millet (YMMM) and malted yellow maize (YMYM) inocula was investigated using an untargeted gas chromatography high‐resolution time of flight mass spectrometry (GC‐HRTOF‐MS)‐based metabolomics. Metabolites in mahewu from different inocula included phenols, fatty acid methyl ester (FAME), benzenes, amides, amines, cyclic compounds, fatty acid ethyl esters (FAEEs), esters, ketones and vitamins which differentiated metabolites identified in raw yellow maize (RYM). Principal component analysis (PCA) showed that the mahewu and related inocula were distinguished across PC1 and PC2. The OPLS‐DA result further intensifies the significant (p ≤ 0.05) metabolite causing variations among samples. This study serves as the first report into the metabolome of yellow maize mahewu from different inocula, serving as a foundation for the quality control of mahewu products for further research.