SUMMARY: A computational homogenization framework is developed in the context of the thermomechanical contact of two boundary layers with microscopically rough surfaces. The major goal is to accurately capture the temperature jump across the macroscopic interface in the finite deformation regime with finite deviations from the equilibrium temperature. Motivated by the limit of scale separation, a two-phase thermomechanically decoupled methodology is introduced, wherein a purely mechanical contact problem is followed by a purely thermal one. In order to correctly take into account finite size effects that are inherent to the problem, this algorithmically consistent two-phase framework is cast within a self-consistent iterative scheme that acts as a first-order corrector. For a comparison with alternative coupled homogenization frameworks as well as for numerical validation, a mortar-based thermomechanical contact algorithm is introduced. This algorithm is uniformly applicable to all orders of isogeometric discretizations through non-uniform rational B-spline basis functions. Overall, the two-phase approach combined with the mortar contact algorithm delivers a computational framework of optimal efficiency that can accurately represent the geometry of smooth surface textures. © 2013 John Wiley & Sons, Ltd.