Members of the P-4 subfamily of P-type ATPases are believed to catalyze flipping of phospholipids across cellular membranes, in this way contributing to vesicle biogenesis in the secretory and endocytic pathways. P-4-ATPases form heteromeric complexes with Cdc50-like proteins, and it has been suggested that these act as beta-subunits in the P-4-ATPase transport machinery. In this work, we investigated the role of Cdc50-like beta-subunits of P-4-ATPases for targeting and function of P-4-ATPase catalytic alpha-subunits. We show that the Arabidopsis P-4-ATPases ALA2 and ALA3 gain functionality when coexpressed with any of three different ALIS Cdc50-like beta-subunits. However, the final cellular destination of P-4-ATPases as well as their lipid substrate specificity are independent of the nature of the ALIS beta-subunit they were allowed to interact with.