In this paper, we derive an effective model for transport processes in periodically perforated elastic media, taking into account, e.g., cyclic elastic deformations as they occur in lung tissue due to respiratory movement. The underlying microscopic problem couples the deformation of the domain with a diffusion process within a mixed Lagrangian/Eulerian formulation. After a transformation of the diffusion problem onto the fixed domain, we use the formal method of two-scale asymptotic expansion to derive the upscaled model, which is nonlinearly coupled through effective coefficients. The effective model is implemented and validated using an application-inspired model problem. Numerical solutions for both, cell problems and macroscopic equations, are investigated and interpreted. We use simulations to qualitatively determine the effect of the deformation on the transport process.