Abstract We study the influence of hot and dense matter in core-collapse supernovae by adopting an up-to-date nuclear equation of state (EOS) based on the microscopic nuclear many-body frameworks. We explore effects of the EOS based on the Dirac–Brückner–Hartree–Fock theory through comparisons with those based on the variational method. We also examine effects of the differences in the composition of nuclei and nucleons by using the same EOS as the variational method but employing two different treatments in computations of nuclear abundances. We perform numerical simulations of core-collapse supernovae adopting the three EOSs. We also perform numerical simulations of the long-term evolution over 70 s of the proto-neutron star cooling. We show that the impacts of different modeling of the composition are remarkable as in those due to different treatments of uniform matter in the gravitational collapse, bounce and shock propagation. The cooling of a proto-neutron star and the resulting neutrino emission are also affected by the compositional difference even if the same treatment is used in computing uniform matter of the EOS.