Controlling the perpendicular magnetic anisotropy (PMA) in thin films has received considerable attention in recent years due to its technological importance. PMA based devices usually involve heavy-metal (oxide)/ferromagnetic-metal bilayers, where, thanks to interfacial spin-orbit coupling (SOC), the in-plane (IP) stability of the magnetisation is broken. Here we show that in V/MgO/Fe(001) epitaxial junctions with competing in-plane and out-of-plane (OOP) magnetic anisotropies, the SOC mediated interaction between a ferromagnet (FM) and a superconductor (SC) enhances the effective PMA below the superconducting transition. This produces a partial magnetisation reorientation without any applied field for all but the largest junctions, where the IP anisotropy is more robust; for the smallest junctions there is a reduction of the field required to induce a complete OOP transition ($$H_\text {OOP}$$
H
OOP
) due to the stronger competition between the IP and OOP anisotropies. Our results suggest that the degree of effective PMA could be controlled by the junction lateral size in the presence of superconductivity and an applied electric field. We also discuss how the $$H_\text {OOP}$$
H
OOP
field could be affected by the interaction between magnetic stray fields and superconducting vortices. Our experimental findings, supported by numerical modelling of the ferromagnet-superconductor interaction, open pathways to active control of magnetic anisotropy in the emerging dissipation-free superconducting spin electronics.