Atg8ylation acts as a temporary scaffold on membranes, recruiting a diverse set of proteins to mediate processes such as cargo sequestration into autophagosomes or intraluminal vesicles, vesicular transport, and membrane remodeling. E3 complexes dictate when and where the ATG8 conjugation machinery is activated, responding to specific signals at the target membrane. Here, we provide new insight into how ATG16-containing E3 complexes target membranes through distinct mechanisms under different cellular conditions. We expand the known repertoire of ATG16 membrane-targeting strategies, uncovering adaptations unique to higher eukaryotic systems.