Autophagy is an intracellular degradation and recycling process which promotes plant acclimation and survival to a wide range of environmental stresses. During autophagy, the formation and maturation of specialized membrane vesicles, named autophagosomes, ensure cargo recognition, sequestration and trafficking to the lytic vacuole. Fusion with the tonoplast delivers, in the vacuolar lumen, a vesicle called autophagic body, which membrane is rapidly broken down thus releasing cargo for degradation. The whole dynamic process of autophagy thus relies on an orchestrated series of membrane remodeling events which underlying molecular mechanisms remain poorly understood. As essential components of biological membranes, lipids have the potential to functionally contribute to several steps of the autophagy pathway. To unravel the nature of lipids and pathways related to lipid dynamics during autophagy, we isolated autophagy compartments and established their molecular cartography. These analyses showed the robustness of their lipid composition, irrespective of autophagy inducing conditions and stage of the pathway. Further, our data highlighted the singular composition of autophagy structures compared to other endomembranes identifying novel potential determinants of membrane formation, architecture and remodeling during autophagy. Notably, we found a soluble lipid-modifying enzyme associating with all compartments of the autophagy pathway: phagophore, autophagosome and autophagic bodies. Upon autophagy inducing conditions, this enzyme which is mostly active at acidic pH, relocalizes from the cytosol to the vacuolar lumen using autophagy as transportation. Further characterization of this protein and its closest homolog points to a potential role in membrane disruption suggesting that they mediate the turn-over of autophagic bodies as the same rate as their delivery, thus efficiently instructing the antepenultimate step of the autophagy pathway.