Metabolomics as a diagnosis tool for plant performance has shown good features for breeding and crop improvement. Additionally, due to limitations in land area and the increasing climate changes, breeding projects focusing on abiotic stress tolerance are becoming essential. Nowadays no universal method is available to identify predictive metabolic markers. As a result, research aims must dictate the best method or combination of methods. To this end, we will introduce the key aspects to consider regarding growth scenarios and sampling strategies and discuss major analytical and data treatment approaches that are available to find metabolic markers of plant performance.