Decellularized extracellular matrix (ECM) biomaterials derived from native tissues and organs are widely used for tissue engineering and wound repair. To boost their regenerative potential, ECM biomaterials can be functionalized via the immobilization of bioactive molecules. To enable ECM functionalization in a chemoselective manner, we have recently reported an effective approach for labeling native organ ECM with the click chemistry-reactive azide ligand via physiologic post-translational glycosylation. Here, using the rat lung as a model, we provide a detailed protocol for in vivo and ex vivo metabolic azide labeling of the native organ ECM using N-Azidoacetylgalactosamine-tetraacylated (Ac4GalNAz), together with procedures for decellularization and labeling characterization. Our approach enables specific and robust ECM labeling within three days in vivo or within one day during ex vivo organ culture. The resulting ECM labeling remains stable following decellularization. With our approach, ECM biomaterials can be functionalized with desired alkyne-modified biomolecules, such as growth factors and glycosaminoglycans, for tissue engineering and regenerative applications.