The management of extensive tracheal resection followed by circumferential replacement remains a surgical challenge. Numerous techniques are proposed with mixed results. Partial decellularization of the trachea with the removal of the mucosal and submucosal cells is a promising method, reducing immunogenicity while preserving the biomechanical properties of the final matrix. Despite many research protocols and proofs of concept, no standardized clinical grade protocol is described. Furthermore, local and systemic biointegration mechanisms of decellularized trachea are not well known. Therefore, in a translational research perspective, this work set up a partial tracheal decellularization protocol in line with Cell and Tissue Products regulations. Extensive characterization of the final product is performed in vitro and in vivo. The results show that the Partially Decellularized Trachea (PDT) is cell‐free in the mucosa and submucosa, while the cartilage structure is preserved, maintaining the biomechanical properties of the trachea. When implanted in the muscle in vivo for 28 days, no systemic inflammation is observed, and locally, the PDT shows an excellent biointegration and vascularization. No signs of graft rejection are observed. These encouraging results confirmed the efficacy of the clinical grade PDT production protocol, which is an important step for future clinical applications.