Experiments and atomic-scale simulations suggest that the transmission of plasticity carriers in deforming amorphous-crystalline nanolaminates is mediated by the biphase interface between the amorphous and crystalline layers. In this paper, we present a micromechanics model for these biphase nanolaminates that describes defect interactions through the amorphous-crystalline interface (ACI). The model is based on an effective-temperature framework to achieve a unified description of the slow, configurational atomic rearrangements in both phases when driven out of equilibrium. We show how the second law of thermodynamics constrains the density of defects and the rate of configurational rearrangements, and apply this framework to dislocations in crystalline solids and shear transformation zones (STZs) in amorphous materials. The effective-temperature formulation enables us to interpret the observed movement of dislocations to the ACI and the production of STZs at the interface as a 'diffusion' of configurational disorder across the material. We demonstrate favorable agreement with experimental findings reported in (Kim et al 2011 Adv. Funct. Mater. 21 4550-4), and demonstrate how the ACI acts as a sink of dislocations and a source of STZs.