Mechanisms underlying the effects of organic amendments on the metabolites in vegetable crop plants remain unclear for the most part. Organic fertilizers are believed to help produce “high quality” vegetables; however, the relationships between organic amendment and vegetable quality are not understood. We took a metabolite profiling approach that comprehensively analyzed both the major and minor constituents of plants. Manure amendments consistently affected the metabolite composition of various vegetable organs in field experiments. Moreover, it was shown that both manure and organic fertilizer amendment caused clear metabolic changes in pot experiments using mizuna (Brassica rapa L. var. Nipponsinica). It is suggested that the amendment of organic matter does indeed influence metabolite composition in vegetables. Further research is needed on the mechanisms responsible for changes in metabolites and on the factors affecting the quality characteristics of foods.