We derive the equation of state of nuclear matter for the quark-meson coupling model taking into account quantum fluctuations of the σ meson as well as vacuum polarization effects for the nucleons. This model incorporates explicitly quark degrees of freedom with quarks coupled to the scalar and vector mesons. Quantum fluctuations lead to a softer equation of state for nuclear matter giving a lower value of incompressibility than would be reached without quantum effects. The in-medium nucleon and σ-meson masses are also calculated in a self-consistent manner. The spectral function of the σ meson is calculated and the σ mass has the value increased with respect to the purely classical approximation at high densities.