The lattice Boltzmann (LB) method is an efficient technique for simulating fluid flow through individual pores of complex porous media. The ease with which the LB method handles complex boundary conditions, combined with the algorithm’s inherent parallelism, makes it an elegant approach to solving flow problems at the sub-continuum scale. However, the realities of current computational resources can limit the size and resolution of these simulations. A major research focus is developing methodologies for upscaling microscale techniques for use in macroscale problems of engineering interest. In this paper, we propose a hybrid, multiscale framework for simulating diffusion through porous media. We use the finite element (FE) method to solve the continuum boundary-value problem at the macroscale. Each finite element is treated as a sub-cell and assigned permeabilities calculated from subcontinuum simulations using the LB method. This framework allows us to efficiently find a macroscale solution while still maintaining information about microscale heterogeneities. As input to these simulations, we use synchrotron-computed 3D microtomographic images of a sandstone, with sample resolution of 3.34 μm. We discuss the predictive ability of these simulations, as well as implementation issues. We also quantify the lower limit of the continuum (Darcy) scale, as well as identify the optimal representative elementary volume for the hybrid LB–FE simulations.