In this paper, we propose a novel, semi-analytic approach for the two-scale, computational modeling of concentration transport in packed bed reactors. Within the reactor, catalytic pellets are stacked, which alter the concentration evolution. Firstly, the considered experimental setup is discussed and a naive one-scale approach is presented. This one-scale model motivates, due to unphysical fitted values, to enrich the computational procedure by another scale. The computations on the second scale, here referred to as microscale, are based on a proper investigation of the diffusion process in the catalytic pellets from which, after continuum-consistent considerations, a sink term for the macroscopic advection–diffusion–reaction process can be identified. For the special case of a spherical catalyst pellet, the parabolic partial differential equation at the microscale can be reduced to a single ordinary differential equation in time through a semi-analytic approach. After the presentation of our model, we show results for its calibration against the macroscopic response of a simple standard mass transport experiment. Based thereon, the effective diffusion parameters of the catalyst pellets can be identified. © 2022, The Author(s).