Plants are the natural source of bioactive compounds used in medicinal and environmental sectors as well as being widely used in commercial and pharmaceutical products. Bioactive plant metabolites are the secondary metabolites produced by plants with the purpose of making them competitive in natural environment. Plant secondary metabolites elicit pharmacological or toxicological effects in man and animals. Besides producing the primary biosynthetic and metabolic compounds associated with plant growth and development, secondary metabolites are produced within the plants and are regarded as the products of biochemical ‘side tracks’ in the plant cells. Several of the bioactive metabolites have contributed various types of important functions in living plants such as providing defence against herbivores, protection against infections, attraction or signalling. Bioactive metabolites also play a role in the complex biological and ecological processes that occur in the rhizosphere through ecosystem-level interactions between plant roots and the soil fauna. Various studies have revealed that bioactive molecular exchanges mediate these interactions as intercellular signal and helps the partner in preparing for various successful interactions. This review article provides a comprehensive analysis of the major bioactive molecules produced by plants, their role in below-ground ecosystem, in remediating the soil ecosystem methodological challenges and novel avenues for their study.