Secondary metabolites produced in food plants influence their quality attributes, such as palatability and functions in health maintenance. Therefore, the control of secondary metabolite contents and composition is important for a number of processes, such as breeding, preservation, distribution, and cooking. Here, we investigated the main secondary metabolites involved in the palatability of savory foods, such as ginger, sweet basil, and tomato. In particular, analysis using gas or liquid chromatography-mass spectrometry (GC or LC-MS) facilitated the structural elucidation of key compounds and enabled the prediction of their biosynthesis. This article reviewed our studies: (1) identification and quantification of pigment compounds in ginger rhizome, (2) biosynthesis of geranial, a key compound of ginger flavor, (3) biosynthetic control of terpene volatiles in different cultivars of sweet basil, and (4) prediction of chemical changes in secondary metabolites by comprehensive analysis using LC-MS.