Secondary metabolites isolated from plants are usually complex mixtures consisting of varieties of active ingredients which need to be characterized. Environmental stresses, including but not limited to drought and salinity, cause significant challenges to crop growth and development. These stresses can disrupt various physiological and biochemical processes within plants, leading to reduced yields and compromised quality of agricultural products and producing different secondary metabolites. Scientific agronomists can utilize environmental stresses to optimize crop traits and improve the quality of resilient crop products. Metabolomics investigations play an important role in identifying the chemical composition of natural products. This technique is a useful tool in agrochemistry and biocontrol for crop protection via biostimulation. Metabolomics plays an essential role in decoding mechanisms of action employed by biostimulants under environmental stresses. It can also assist in understanding the plant-microorganism interaction and lead to exploring the biocontrol products under biotic and abiotic stresses in the crop industry. Lipidomics, sensomics, hormonomics and some other functional metabolomic-based techniques can assist in improving the quality of stressed crops. This review discusses a metabolomics analysis of three vital African cereals (maize, rice and wheat) to demonstrate the potential value of metabolomic investigation in enhancing the nutritional quality and quantity of these cereals under environmental stresses.