Both enzymatically and non-enzymatically generated oxylipins fulfill signalling functions in plant responses to biotic and oxidative stress on the cellular level. We studied the impact of two different exogenously applied cyclopentenone-oxylipins on the proteome of Arabidopsis thaliana leaves: the enzymatically formed 12-oxo-phytodienoic-acid, a member of the jasmonate family of mediators, and A(1)-phytoprostane generated by a free-radical mechanism upon biotic and oxidative stress. Infiltration of leaves with these oxylipins led to induction of classical stress proteins like chaperones as well as enzymes connected to the cellular redox and detoxification systems. A large proportion of the regulated proteins are localized in chloroplasts where these oxylipins are formed. Furthermore, we show that cyclopentenone-oxylipins spontaneously react with several proteins and glutathione in vitro and in vivo. Conjugation to the glutathione sulfhydryl group is a reversible process that is also catalysed by glutathione-S-transferases. In vitro, an oxidative stress inducible glutathione-S-transferase, GST6, localized both in plastids and the cytosol can be covalently modified and partially inactivated by several cyclopentenone-oxylipins.