In this work, the structure and stress evolution in Co/Au and Co/Cu two-layer systems during deposition were studied. The growth of this system is evaluated by employing molecular dynamic simulations with potentials based on the embedded atom method theory. We used the kinematical scattering theory and the Ackland-Jones bondangle method to the structural characterisation of deposited layers. In both systems, only compressive stress is observed during the deposition process and process relaxation of stress is visible. In Co/Au systems, creation of grains and grain boundaries is observed.