A total of 72 plant extracts were tested in vitro for their ability to inhibit the mycelial growth of Lasiodiplodia theobromae and Colletotrichum musae the causal agents of crown rot disease of banana. The results showed that the leaf extract of Zimmu (an interspecific hybrid of Allium cepa L. × Allium sativum L.) and tuber extract of Zehneria scabra recorded maximum inhibition of mycelial growth and spore germination of both the test pathogens. The dipping of banana fruits in Zimmu leaf extract at 25% conc. exhibited 100% inhibition of crown rot disease in cold storage (14 °C) up to 35 days and increased the shelf life to 64 days. However, at room storage (28 ± 2 °C), the same treatment exhibited 86% inhibition of crown rot disease up to 12 days. It was found that the treatment of banana fruits with Zimmu leaf extract did not alter the organoleptic properties of banana. The biochemical analysis of banana fruits treated with Zimmu leaf extract showed significant increase in phenylalanine ammonia-lyase (PAL), chitinase and β-1,3-glucanase activities and enhanced accumulation of phenolic compounds compared to other treatments. These findings suggest that the effect of Zimmu leaf extract on crown rot disease may be associated with the direct fungi toxic property against the test pathogens and elicitation of defense related compounds in banana fruits.