Experimental studies show that metal–ceramic multilayers can have high strength, high strain hardening and measurable plasticity when the ceramic layer is a few nanometers thick. Using molecular dynamics simulations we studied deformation mechanisms in metal–ceramic multilayers and the role of interface structure and layer thickness on mechanical behavior. NbC/Nb multilayers were investigated numerically using the molecular dynamics (MD) method with empirical interatomic potentials. The interface dislocation structure was characterized by combining MD simulations and atomically informed Frank–Bilby theory. Two sets of pure edge misfit dislocations have been identified. Plastic deformation in NbC/Nb multilayers commences first in the metal layers by nucleation and glide of lattice dislocations initiating from interface misfit dislocations. These dislocations glide in the Nb layer and are deposited at the interface. The deposited dislocations facilitate slip transmission from the Nb layer to the NbC layer. The critical strain corresponding to dislocation nucleation is insensitive to layer thickness but depends on interface dislocation structure. The strain hardening and the peak flow strength of NbC/Nb multilayers are associated with the slip transmission from Nb to NbC, and are correlated to the interfacial dislocations, Nb layer thickness, and NbC layer thickness. The flow strength decreases with increasing Nb layer thickness and decreasing the NbC layer thickness.