Endophytes are ubiquitous and grow in plant tissues without causing any harmful effects to the host. They include different groups of microorganisms such as bacteria, fungi and actinomycetes. Along with the host plants, the existing endophytes also co-evolve after a long relationship between them. Host plant-endophyte interaction is similar to that of plant growth promoting microbes as they induce the growth of the host plant and increase resilience against biotic and abiotic stresses. The interaction of plant endophytes at the molecular level and the effect of endophytes on host gene expression is a new field of study and are still rarely explored. Endophytes act as a promising resource of many invaluable bioactive secondary metabolites. Some of these bioactive compounds include alkaloids, polyphenols, sterols, xanthones, terpenoids, flavones, coumarins, polyketides, quinones, saponins, tannins, benzopyrones, dibenzofurans. These secondary metabolites are beneficial for agriculture, industrial and pharmacological purposes. As endophytes have beneficial effects in sustainable agriculture, plant disease management, pharmaceuticals, industry and environmental management in an eco-friendly way, thus improving the strategy of application of endophytes as biological agents in every aspect of our life is a very challenging field of research. Our aim in this present review is to focus on plant-endophyte interactions and their various dimensions in order to address some future possibilities for expediting the bioactive secondary metabolite production.