SummarySoaking of soybeans is an essential step in tempe fermentation. Owing to the uncontrolled microflora, spontaneous soaking during tempe production leads to inconsistencies in tempe quality. Common methods to control it include the addition of acids or microbial starters. Despite knowing the benefits, their impact on tempe's composition was less understood. In this study, prior to tempe fungal fermentation, soybeans were soaked with Lactiplantibacillus plantarum NBRC 101978 and Pichia burtonii NBRC 0844. Tempe samples were subjected to comprehensive analysis using a widely targeted gas chromatography–mass spectrometry (GC–MS) metabolomics approach and evaluation of physical characteristics. A total of 100 metabolites of sugars, amino acids, fatty acids, and organic acids were annotated in all samples. Principal component analysis (PCA) explaining 47.6% of the variance showed that microbial interventions led to alterations in the metabolome of all samples, including the accumulation of amino acids in lactic acid bacteria (LAB)‐soaked soybean tempe and tyramine in yeast‐soaked soybean tempe. Unlike chemically added soaked soybean tempe, microbial intervention significantly reduced the relative intensity levels of several sugars by more than twofold. Furthermore, microbial interventions in the tempe‐soaking step significantly elevated the levels of bioactive metabolites more than twofold. The introduction of microbial interventions in the tempe‐soaking step also influences the physical characteristics of the end product. These findings merit further consideration for tempe development and the food industry.
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