Researchers and pharmacists are replacing synthetic chemicals with natural resources for drug manufacturing purposes. Plants produce secondary metabolites which possess antibacterial, antifungal, anticancer, antimalarial, antiprotozoal, antioxidant properties, etc. These metabolites are beneficial for plant growth and development by protecting them from harmful UV irradiation, insects and extreme temperatures. Phytochemicals with bioactive potential like salicylates found in the willow tree bark for reducing inflammation, lycopene- a phytochemical found in tomato to fight against cardiovascular diseases and lung cancers. In general, medicinal plants harbour endophytes (the group of microorganisms inhabiting within the plant host for a particular life cycle without harming the host) which are a prolific source of secondary metabolites and phytochemical production. Production of these metabolites by the endophytes from medicinal plants has shifted the focus from using chemicals to natural resources for drug discovery. The microbial biotransformation is an alternative method for the production of bioactive compounds. A single endophyte is responsible for various other secondary metabolites like terpenoids, steroids, alkaloids, flavonoids, etc. Hence, phytochemicals with novel structures can be exploited in the field of medicine for new drug discovery. © Springer Nature Singapore Pte Ltd. 2020.