Metabolomics is an omics technology that is extremely valuable to analyze all small-molecule metabolites in organisms. Recent advances in analytical instrumentation, such as mass spectrometry combined with data processing tools, chemometrics, and spectral data libraries, allow plant metabolomics studies to play a fundamental role in the agriculture field and food security. Few studies are found in the literature using the metabolomics approach in soybean plants on biotic stress. In this review, we provide a new perspective highlighting the potential of metabolomics-based mass spectrometry for soybean in response to biotic stress. Furthermore, we highlight the response and adaptation mechanisms of soybean on biotic stress about primary and secondary metabolism. Consequently, we provide subsidies for further studies of the resistance and improvement of the crop.