Eukaryotic cells must constantly degrade both intracellular and extracellular material to maintain cellular and organismal homeostasis. Two engulfment pathways, autophagy and phagocytosis, contribute to the turnover of intracellular and extracellular substrates by delivering material to the lysosome. Historically these are thought to be separate pathways, but recent studies have revealed the direct participation of autophagy proteins in phagocytosis. Autophagy proteins lipidate LC3 onto phagosomes and other macroendocytic vacuole membranes, and are required for lysosomal degradation of engulfed cargo, demonstrating an autophagosome-independent role for autophagy proteins in mediating the turnover of extracellular substrates. This review discusses the biological systems in which autophagy proteins have been found to regulate lysosome fusion to non-autophagic membranes.