Multi-element analysis including stable isotopes can be used as a possible indicator for food safety and security. For the certification of geographical origin, the analytical methods can be performed in two ways: one where multivariate analysis is used to determine the concentrations of such omnipresent elements as Al, Ca, Cl, Mg, Mn, Fe and Zn, and one that focuses on such special elements as the stable isotope ratios of Sr, O, and H. For the certification of production methods, especially those regarding organic products, δ 15 N values could be a potential indicator, particularly in such protected cultivations as in a plant factory (advanced-type greenhouse horticulture). Because the accuracy of these values is affected by production conditions, the δ 15 N values of products can be predicted more accurately under controlled conditions, such as in a plant factory using δ 15 N-evaluated fertilizer, medium, and water. Non-destructive systems have been developed for measuring both the level of elements in a product and the production environment, such as soil conditions. In the near future, the results of chemically analyzed and those of non-destructively analyzed elemental composition will become interconnected to non-destructively certify the geographical origin and production method of agricultural products. All these destructive methods have been used to a limited extent for practical regulation as an analysis guideline; however, a combined system involving the use of the newly developed detector (nondestructive), data collection, and analysis using artificial intelligence could address the issue of falsely labeled products for practical application. Particularly in a plant factory, production is controlled and regulated, allowing the tracing of products from the farm to the table. In this context, the greenhouse production system would be an advanced example for the practical use of food safety combined with analytical chemistry and information communication technology.