In the endolysosomal pathway, endosomes undergo a maturation process that involves a reduction in their luminal pH and the acquisition of Rab7, as well as sequestration of ubiquitylated cargo within intraluminal vesicles (ILVs), priming them for fusion with the lysosomes. Budding yeast strains that are deficient for PI(3,5)P2 or the ubiquitin hydrolase Doa4 exhibit defects in the sorting of ILV cargoes, but it is unclear whether this reflects indirect effects owing to mis-regulated membrane trafficking or whether these factors actively participate in cargo sorting. In their paper, Greg Odorizzi and co-workers (Wilson et al., 2021) now show that these cargo-sorting defects are restored in mutants that disrupt Vph1, a subunit of the vacuolar H+-ATPase (V-ATPase) that acidifies late endosomes and vacuoles. As shown here, loss of Vph1 function in cells that lack either Doa4 or Fab1, the enzyme responsible for PI(3,5)P2 synthesis, increases the abundance of endosomes and impairs the recruitment of Ypt7, the yeast Rab7 homolog, to the vacuolar membrane, thus attenuating fusion with endosomes. On the basis of their findings, the authors suggest that in the absence of PI(3,5)P2, fusion occurs aberrantly prior to the completion of ILV cargo sorting. This study thus points to a role for V-ATPase in coordinating the removal of cargoes from ILVs with membrane fusion, and further studies will address the role of cargo ubiquitylation in this process.