Lignin has emerged as an attractive alternative in the search for more eco‐friendly and less costly materials for enzyme immobilization. In this work, the terephthalic aldehyde‐stabilization of lignin is carried out during its extraction to develop a series of functionalized lignins with a range of reactive groups (epoxy, amine, aldehyde, metal chelates). This expands the immobilization to a pool of enzymes (carboxylase, dehydrogenase, transaminase) by different binding chemistries, affording immobilization yields of 64–100 %. As a proof of concept, a ω‐transaminase reversibly immobilized on polyethyleneimine‐lignin is integrated in a packed‐bed reactor. The stability of the immobilized biocatalyst is tested in continuous‐flow deamination reactions and maintains the same conversion for 100 cycles. These results outperform previous stability tests carried out with the enzyme covalently immobilized on methacrylic resins, with the advantage that the reversibility of the immobilized enzyme allows recycling and reuse of lignin beyond the enzyme inactivation. Additionally, an in‐line system also based on lignin is added into the downstream process to separate the reaction products by catch‐and‐release. These results demonstrate a fully closed‐loop sustainable flow‐biocatalytic system based exclusively on lignin.