We develop a model of transport in multiscale porous media which accounts for adsorption in the different porosity scales. This model employs statistical mechanics to upscale molecular simulation and describe adsorption and transport at larger time and length scales. Using atom-scale simulations, which capture the changes in adsorption and transport with temperature, pressure, pore size, etc., this approach does not assume any adsorption or flow type. Moreover, by relating the local chemical potential μ(r) and density ρ(r), the present model accounts for adsorption effects and possible changes in the confined fluid state upon transport. This model constitutes a bottom-up framework of adsorption and transport in multiscale materials as it (1) describes the adsorption-transport interplay, (2) accounts for the hydrodynamics breakdown at the nm scale, and (3) is multiscale.