A number of natural polymer biomaterial‐based nerve guidance conduits (NGCs) are developed to facilitate repair of peripheral nerve injuries. Cross‐linking ensures mechanical integrity and desired degradation properties of the NGCs; however, common methods such as formaldehyde are associated with cellular toxicity. Hence, there is an unmet clinical need for alternative nontoxic cross‐linking agents. In this study, collagen‐based NGCs with a collagen/chondroitin sulfate luminal filler are used to study the effect of cross‐linking on mechanical and structural properties, degradation, biocompatibility, and immunological response. A simplified manufacturing method of genipin cross‐linking is developed, by incorporating genipin into solution prior to freeze‐drying the NGCs. This leads to successful cross‐linking as demonstrated by higher cross‐linking degree and similar tensile strength of genipin cross‐linked conduits compared to formaldehyde cross‐linked conduits. Genipin cross‐linking also preserves NGC macro and microstructure as observed through scanning electron microscopy and spectral analysis. Most importantly, in vitro cell studies show that genipin, unlike the formaldehyde cross‐linked conduits, supports the viability of Schwann cells. Moreover, genipin cross‐linked conduits direct macrophages away from a pro‐inflammatory and toward a pro‐repair state. Overall, genipin is demonstrated to be an effective, safe, biocompatible, and anti‐inflammatory alternative to formaldehyde for cross‐linking clinical grade NGCs.