Significance Far-red (FR) insensitive 219 (FIN219) is the main jasmonate (JA)-amido synthetase that activates the systemic synthesis of bioactive JAs in Arabidopsis . FIN219 is involved in FR light signaling and interacts with another signaling component, FIN219-interacting protein 1 (FIP1). To extend our understanding of the regulatory mechanism between FR light signaling and the JA response, we determine the crystal structures of the FIN219–FIP1 complex with substrates and show that interaction with FIP1 triggers enhanced activity of FIN219. FIN219 conformational changes driven by FIP1 are observed in the C-terminal domain and show a relatively occluded form of the active site. By measuring the FIN219–FIP1 interaction and adenylation function, this study reveals that FIP1 may regulate FIN219 activity and further alters the level of JA signaling.