We are motivated to model PE‐CVD (plasma enhanced chemical vapor deposition) processes for metallic bipolar plates, and their optimization for depositing a heterogeneous layer on the metallic plate. Moreover a constraint to the deposition process is a very low pressure (nearly a vacuum) and a low temperature (about 400 K). The contribution of this paper is to derive a multiphysics system of multiple physics problems that includes some assumptions to simplify the complicate process and allows of deriving a computable mathematical model without neglecting the real‐life processes. To model the gaseous transport in the apparatus we employ mobile gas phase streams, immobile and mobile phases in a chamber that is filled with porous medium (plasma layers). Numerical methods are discussed to solve such multi‐scale and multi phase models and to obtain qualitative results for the delicate multiphysical processes in the chamber. We discuss a splitting analysis to couple such multiphysical problems. The verification of such a complicated model is done with real‐life experiments for single species. Such numerical simulations help to economize on expensive physical experiments and obtain control mechanisms for the delicate deposition process.