When neutrino masses arise from the exchange of neutral heavy leptons, as in most seesaw schemes, the effective lepton mixing matrix N describing neutrino propagation is non-unitary, hence neutrinos are not exactly orthonormal. New CP violation phases appear in N that could be confused with the standard phase δCP characterizing the three neutrino paradigm. We study the potential of the long-baseline neutrino experiment DUNE in probing CP violation induced by the standard CP phase in the presence of non-unitarity. In order to accomplish this we develop our previous formalism, so as to take into account the neutrino interactions with the medium, important in long baseline experiments such as DUNE. We find that the expected CP sensitivity of DUNE is somewhat degraded with respect to that characterizing the standard unitary case. However the effect is weaker than might have been expected thanks mainly to the wide neutrino beam. We also investigate the sensitivity of DUNE to the parameters characterizing non-unitarity. In this case we find that there is no improvement expected with respect to the current situation, unless the near detector setup is revamped.