Formation of functional thin films for nanoelectronics and magnetic data storage via thermally induced diffusion-driven structural phase transformations in multilayer stacks is a promising technology-relevant approach. Ferromagnetic thin films based on CoPt alloys are considered as a material science platform for the development of various applications such as spin valves, spin orbit torque devices, and high-density data storage media. Here, we study diffusion processes in Pt-Co-based stacks with the focus on the effect of layers inversion (Pt/Co/substrate vs. Co/Pt/substrate) and insertion of an intermediate Au layer on the structural transitions and magnetic properties. We demonstrate that layer stacking has a pronounced effect on the diffusion rate at temperatures, where the diffusion is dominated by grain boundaries. We quantify effective diffusion coefficients, which characterize the diffusion rate of Co and Pt through the interface and grain boundaries, providing the possibility to control the homogenization rate of Pt-Co-based heterostructures. The obtained values are in the range of 10-16 – 10-13 cm2/s for temperatures of 150 °C – 350 °C. Heat treatment of thin-film samples results in the coercivity enhancement, which is attributed to short-range chemical ordering effects. We show that introducing an additional Au intermediate layer leads to an increase of the coercive field of the annealed samples due to a modification of exchange coupling between the magnetic grains at the grain boundaries.