In a process contributing to the innate immunity of higher plants, Arabidopsis thaliana cyclophilin ROC1 induces the self-cleavage of Pseudomonas syringae putative cysteine protease AvrRpt2, triggering limited cleavage of A. thaliana RIN4, a negative regulator of plant immunity. We report an increase in AvRpt2 activity in hydrolysis of decapeptide substrates at -GG- sites of more than 5 orders of magnitude, in the presence of cyclophilin-like peptidyl prolyl cis/trans isomerases including ROC1 or hCyp18. Both full-length AvrRpt2 and its 21 kDa self-cleavage product (AvrRpt2(72-255)) were found to be equally active under these conditions. In contrast to classical isomer-specific proteolysis, inertness toward cleavage of a cis/trans prolyl bond isomer at the substrate P4 subsite is not the cause of cyclophilin-mediated activation of the proteolytic reaction. Monitoring single- and double-jump kinetics of proteolytic reactions in the presence of the PPIase inhibitor cyclosporin A revealed that the cis/trans ratio of potentially relevant prolyl bonds of AvrRpt2(72-255) remained the same in the functionally inactive state of AvrRpt2(72-255) and the productive AvrRpt2(72-255)-cyclophilin-substrate complex.