The present work reports the effect of salt treatment on Hyssopus officinalis growth, essential oil (EO) yield and composition and the antiparasitic effects of the oil against the plant (Phytomonas davidi and Meloidogyne javanica) and human (Trypanosoma cruzi) parasites. Our results showed that salinity decreased plant growth and EO yield of hydroponically cultivated plants of H. officinalis with increasing NaCl levels. Salinity also induced changes in the chemical composition of treated hyssop EOs, decreasing the monoterpene and increasing the sesquiterpene groups. The oxygenated monoterpenes, represented primarily by isopinocamphone and pinocarvone, were the major chemical class. The EOs from treated H. officinalis showed moderate antiparasitic effects against T. cruzi, independent of the salt treatment, stronger salt-dependent effects on P. davidi and also a high salt-dependent nematicidal activity against M. javanica. Therefore, a moderate salt treatment reduced plant growth and EO yield but increased its biocidal effects on plant parasites (P. davidi and M. javanica).