A novel process-based methodology is proposed for the stochastic reconstruction and accurate characterisation of Carbon fiber-based matrices, which are commonly used as Gas Diffusion Layers in Proton Exchange Membrane Fuel Cells. The modeling approach is efficiently complementing standard methods used for the description of the anisotropic deposition of carbon fibers, with a rigorous model simulating the spatial distribution of the graphitized resin that is typically used to enhance the structural properties and thermal/electrical conductivities of the composite Gas Diffusion Layer materials. The model uses as input typical pore and continuum scale properties (average porosity, fiber diameter, resin content and anisotropy) of such composites, which are obtained from X-ray computed microtomography measurements on commercially available carbon papers. This information is then used for the digital reconstruction of realistic composite fibrous matrices. By solving the corresponding conservation equations at the microscale in the obtained digital domains, their effective transport properties, such as Darcy permeabilities, effective diffusivities, thermal/electrical conductivities and void tortuosity, are determined focusing primarily on the effects of medium anisotropy and resin content. The calculated properties are matching very well with those of Toray carbon papers for reasonable values of the model parameters that control the anisotropy of the fibrous skeleton and the materials resin content. •We propose a novel algorithm for resin deposition in GDLs.•We obtain microscale information using X-ray micro-CT measurements.•We study the transport properties of realistic reconstructed GDLs.•We focus primarily on the effects of resin content and medium anisotropy.•Our numerical calculations compare very good with experimental data.