The performance of the polymer electrolyte membrane (PEM) fuel cell is governed by a complex interaction of the structure of the membrane electrode assembly (MEA), cell compression, and operating parameters. Adequate cell compression for improved current collection and gas sealing can structurally deform MEA with adverse consequences. Non-uniform MEA compression exerted by the flow-field design and arrangement induces heterogeneous transport properties. Hence, understanding morphological evolution and effective transport properties as an effect of MEA compression is an important factor for improving fuel cell performance and durability. In this paper, an X-ray computed tomography study of the entire MEA compression is presented, comprising of gas diffusion and microporous layers, catalyst layers, and the electrolyte membrane, subjected to non-uniform compression under two distinct flow-field arrangements. This study presents a comprehensive dataset of the heterogeneous effective properties required for robust computational modelling; including porosity, permeability, tortuosity, and diffusivity, along with the extent of blocking of the flow channel due to cell compression and effect of compression on the structural properties of the membrane.