The quark-meson coupling (QMC) model incorporates quark degrees of freedom into the relativistic mean-field (RMF) framework, distinguishing it from traditional quantum hadrodynamics (QHD), which treats nucleons as point-like particles. In this work, we implement the QMC model within the DaeJeon Boltzmann-Uehling-Uhlenbeck (DJBUU) transport code to investigate its applicability to intermediate-energy heavy-ion collisions. We simulate ¹⁹⁷Au+¹⁹⁷Au collisions at a beam energy of 400 A MeV using both QHD and QMC and find that both approaches yield comparable results for bulk observables such as transverse and directed flow, with good agreement with experimental data. To further assess the model performance, we study pion production in neutron-rich (¹³²Sn+¹²⁴Sn) and less neutron-rich (¹⁰⁸Sn+¹¹²Sn) systems at 270 A MeV. In contrast to the QHD case, reproducing the observed pion yields and charge ratios within the QMC framework requires a slightly reduced density-dependent suppression in the in-medium Δ production cross-section. These results demonstrate that the QMC model can be effectively integrated into transport simulations.