We study the quantum transition from an antiferromagnet to a superconductor in a model for electron- and hole-doped cuprates by means of a variational cluster perturbation theory approach. In both cases, our results suggest a tendency towards phase separation between a mixed antiferromagnetic-superconducting phase at low doping and a pure superconducting phase at larger doping. However, in the electron-doped case the energy scale for phase separation is an order of magnitude smaller than for hole doping. We argue that this can explain the different pseudogap and superconducting transition scales in hole- and electron-doped materials.