Peptide-based hydrogels have been widely used for both tissue engineering approaches and therapeutic drug delivery mainly thanks to their tissue-like water content and tunable physicochemical properties. In particular, the modulation of the hydrogel chemical structure influences hydrogel properties. The most common approach for tuning hydrogel properties in terms of cell adhesion or release efficiency of entrapped compounds is chemical crosslinking. In this study Fluorenylmethyloxycarbonyl (Fmoc)-tripeptide hydrogels were synthetized in the presence of Genipin as a crosslinker using a biocatalyzed reverse hydrolysis reaction occurring between FmocPhe and Phe(2) in the presence of Pseudornonas fiuorescens lipase. Infrared Attenuated Total Reflection (IR-ATR), Liquid Chromatography coupled to Mass Spectrometry (LC-MS) and Scanning Electron Microscopy (SEM) investigations were used to investigate the interaction of Genipin with Fmoc-peptides as well as with their precursors. The whole instrumental platform allowed us to identify two crosslinked products that had never been reported previously and provide deeper insight into the use of natural crosslinkers for peptide hydrogel modification.