PURPOSE: Bronchiolitis obliterans (BOS) remains a major cause of death for lung transplant recipients, and mechanisms that drive BOS remain poorly understood. Genetically encoded deficiencies in mitophagy, a specialized autophagy that targets the removal of damaged mitochondria, have been shown to promote Parkinson's disease, but it is unclear if they play a role in other chronic diseases. Recent work has shown that the rs2241880 mutation in the autophagy regulator ATG16L1 leads to protein instability resulting in deficiency of ATG16L1 in monocyte-derived macrophages. We previously observed that human lung recipients that are carriers of rs2241880 had faster BOS development. Here, we analyzed the effects of ATG16L1 deficiency in monocyte-derived alveolar macrophages (Mo-AM) in a mouse orthotopic lung transplant model of BOS. METHODS: CD11cCre ATG16L1flox/flox (ATG16L1Δ/Δ) and control CD11cCre recipients received major MHC-mismatched FVB lungs and were immunosuppressed to induce acceptance. Following induced epithelial injury, allografts were assessed for obliterative airway lesions (OB) for up to 28 days. Intragraft Mo-AM were analyzed for bulk RNA sequencing and by flow cytometry (FACS) for mitochondrial mass and ROS production. Mitophagic flux was visualized by confocal microscopy using Mt-kiema mitophagy reporter mice. Mo-AM were characterized metabolically using a Seahorse XF analyzer. RESULTS: When compared to controls, CD11cCre ATG16L1flox/flox recipients showed severe and accelerated OB development. RNAseq analysis of ATG16L1Δ/Δ Mo-AM demonstrated a loss of transcripts that encode several subunits of mitochondria electron complex I, II and V. Confocal and FACS analysis revealed attenuated mitophagic flux, high mitochondrial mass and elevated ROS production in ATG16L1Δ/Δ Mo-AM. In line with these observations were decreased maximal mitochondrial respiratory capacity, lower mitochondrial ATP production and increased utilization of glycolysis- consistent with the metabolic adaptation of an M1 inflammatory phenotype. CONCLUSION: Collectively, these data reveal a new role for ATG16L1 as a regulator of mitochondrial quality control with implications for lung recipients that carry the ATG16L1 rs2241880 mutation.