The inability to monitor the molecular trajectories of whole organs throughout the clinically relevant ischemic interval is a critical problem underlying the organ shortage crisis. Here, we report a novel technique for fabricating manufacturing conformal microfluidic devices for organ interface. 3D conformal printing was leveraged to engineer and fabricate novel organ-conforming microfluidic devices that endow the interface between microfluidic channels and the organ cortex. Large animal studies reveal microfluidic biopsy samples contain rich diagnostic information, including clinically relevant biomarkers of ischemic pathophysiology. Overall, these results suggest microfluidic biopsy via 3D printed organ-conforming microfluidic devices could shift the paradigm for whole organ preservation and assessment, thereby relieving the organ shortage crisis through increased availability and quality of donor organs.