In the last decades, consumers have become increasingly interested in organic products, and they strongly demand reliability in the traceability of the organic products they buy and eat. Several research methods have been developed in the last decades to study inexperienced and reliable systems and to assess the authenticity of products obtained using organic cultivation practices. The monitoring of some chemical compounds, originating from primary and/or secondary metabolism, in horticultural organic and conventional products has shown the diversity generated using the two production approaches. The difference in fertilization practices has been also shown to have an effect on the isotopic distribution of some elements, with particular reference to nitrogen. An integrated system is proposed to evaluate the validity of organic goods using collected isotopic data and other chemical and biological parameters. This approach is intended to be coupled to the application of chemometric multivariate analysis on quality and nutraceutical parameters combined with isotopic data. Indeed, this will give the opportunity to discriminate organic from conventional products based on different isotopic signatures, due to the different nitrogenous sources, combined with the qualitative profile of the crops, which are significantly affected by the different agronomic treatments. The main perspectives of the presented integrated approach, based on the combined use of chemometric and analytical tools, are linked to the feasibility of applying a reliable system for traceability. This will authenticate productions obtained using organic fertilizers (organic agriculture) with respect to those obtained with the use of synthetic fertilizers (conventional agriculture), protect and valorize virtuous farmers and support political stakeholders and decision-makers to counteract food fraud.