The Universe may contain sufficiently small size matter-antimatter domains at temperatures of a few hundred MeV, without violating the success of big bang nucleosynthesis. We demonstrate that this possibility enhances the keV scale sterile neutrino production and may lead to its abundance consistent with the observable energy density of dark matter (DM). Assuming that the quantum chromodynamics (QCD) phase transition is of the first order we argue that it may lead to the separation of matter and antimatter, creating temporarily macroscopic domains occupied by hadronic matter and quark-gluon plasma. In these domains an excess of baryons over antibaryons and vice versa largely can exceed the average baryon and lepton asymmetries of the Universe. We discuss several scenarios of matter-antimatter separation at the QCD phase transition and the production of DM sterile neutrinos in each of them. One of the possibilities requires the presence of lepton asymmetry of the Universe, which can be smaller than that needed for the DM correct abundance in the homogeneous case. Another, the more speculative one, is related to the Omnes phase transition and does not require lepton asymmetries.