Microbial secondary metabolites which are low molecular weight bioactive compounds, are beneficial to agriculture in several ways. However, less attention has been paid to fungal secondary metabolites compared to those from bacteria. An assortment of secondary metabolites produced by the fungi during their growth and development are broadly categorised into antibiotics, alkaloids, mycotoxins, alcohols and fatty acids, which are regulated by various metabolic pathways. These metabolites exhibit marked variations in their chemical structures and biological activities. Though not important for the fungal growth and reproduction, these metabolites determine the interaction between the host and its environment, playing important role in several survival functions. These metabolites are also extensively used in the field of medicine and agriculture as antibiotics, antitumor and antidiarrheal drugs, immunosuppressants, agricultural herbicides, fungicides, bio-insecticides, plant growth stimulators etc. Penicillin, a well-studied secondary metabolite obtained from Penicillium sp. was the first antibiotic exhibiting broad spectrum of activities. This species also produces antimalarial (Benzomalvin C), anti-tumour (oxaline), anticholesterolemics (Pravastatin) agents and several other molecules with health benefitting effects. Other fungal species like Trichoderma viride, Monascus ruber and Aspergillus terreus are also known to produce compounds with antimicrobial and anti-cancer properties. On agriculture front, Penicillium, Aspergillus and Trichoderma species are known to have biocontrol properties against plant pathogens, with important role in phytoremediation. Using secondary metabolites obtained from fungal organisms for crop improvement can reduce dependence on synthetic substances and impart eco-friendly approach towards sustainable agriculture.