In memory of our colleague and friend Professor François Diederich Chemical ligation reactions of functional groups that can be masked with two-photon labile protecting groups provide a powerful technology for the three-dimensional patterning of molecules-including proteinsonto hydrogel scaffolds. In order to utilize readily prepared hydrogels constructed by the potassium acyltrifluoroborate (KAT)-hydroxylamine amide formation ligation for two-photon patterning, we have developed a unique post-polymerization protecting group strategy through the reaction of KATs and dithiols in water and deprotection by two-photon excitation. After precise 3D spatially confined light irradiation, the unprotected KATs undergo ligations with hydroxylamine-functionalized superfolder GFP and sulforhodamine B for the composition of three-dimensional patterns.