Metabolomics is paramount for precision agriculture. Knowing the metabolic state of the vine and its implication for grape quality is of outermost importance for viticulture and wine industry. The MetBots system is a metabolomics precision agriculture platform, for automated monitoring of vineyards, providing geo-referenced metabolic images that are correlated and interpreted by an artificial intelligence self-learning system for aiding precise viticultural practices. Results can further be used to analyze the plant metabolic response by genome-scale models. In this research, we introduce the system main components: (i) robotic platform; (ii) autonomous navigation; (iii) sampling arm manipulation; (iv) spectroscopy systems; and (v) non-invasive, real-time metabolic hyper-spectral imaging monitoring of vineyards. The full potential of the Metbots system is revealed when metabolic data and images are analyzed by big data AI and systems biology vine plant models, establishing a new age of molecular biology precision agriculture.