Transport equations for composite nucleons and deconfined quarks in quark-nuclear matter (QNM) are derived. QNM is a many-body system containing hadrons and deconfined quarks. The starting point is a microscopic quark-meson coupling (QMC) Hamiltonian with a density-dependent quark-quark interaction. An effective quark-hadron Hamiltonian containing canonical hadron and quark field operators is constructed using a mapping procedure. For high densities, the effective Hamiltonian contains interactions that lead to quark decon- finement. Transport equations of the Ueling-Ullenbeck-Vlasov type for quarks and nucleons are obtained using standard many-body techniques with the effective quark-hadron Hamiltonian.