Plants produce short-chain aldehydes and hydroxy fatty acids, which are important industrial materials, through the lipoxygenase pathway. Based on the information that lipoxygenase activity is up-regulated in tobacco leaves upon infection with tobacco mosaic virus (TMV), we introduced a melon hydroperoxide lyase (CmHPL) gene, a tomato peroxygenase (SlPXG) gene and a potato epoxide hydrolase (StEH) into tobacco leaves using a TMV-based viral vector system to afford aldehyde and hydroxy fatty acid production. Ten days after infiltration, tobacco leaves infiltrated with CmHPL displayed high enzyme activities of 9-LOX and 9-HPL, which could efficiently transform linoleic acid into C9 aldehydes. Protein extracts prepared from 1 g of CmHPL-infiltrated tobacco leaves (fresh weight) in combination with protein extracts prepared from 1 g of control vector-infiltrated tobacco leaves (as an additional 9-LOX source) produced 758 ± 75 μg total C9 aldehydes in 30 min. The yield of C9 aldehydes from linoleic acid was 60%. Besides, leaves infiltrated with SlPXG and StEH showed considerable enzyme activities of 9-LOX/PXG and 9-LOX/EH, respectively, enabling the production of 9,12,13-trihydroxy-10(E)-octadecenoic acid from linoleic acid. Protein extracts prepared from 1 g of SlPXG-infiltrated tobacco leaves (fresh weight) in combination with protein extracts prepared from 1 g of StEH-infiltrated tobacco leaves produced 1738 ± 27 μg total 9,12,13-trihydroxy-10(E)-octadecenoic acid isomers in 30 min. The yield of trihydroxyoctadecenoic acids from linoleic acid was 58%. C9 aldehydes and trihydroxy fatty acids could likely be produced on a larger scale using this expression system with many advantages including easy handling, time-saving and low production cost.