In this work, the diffusion process of sodium (Na) in molybdenum (Mo) thin films while it was deposited on soda lime glass (SLG) was studied. A small amount of oxygen was present in the chamber while the direct-current (DC) magnetron sputtering was used for the deposition. The substrate temperatures were varied to observe its effect. Such molybdenum films, with or without oxidations, are often used in thin film solar cells, either as back contact or as hole transport layers. Secondary ion mass spectrometry (SIMS) was used to quantify the concentration of the species. A grain diffusion mechanistic model incorporating the effect of grain and grain boundary geometrical shape and size was developed. The model was used to provide an in-depth theoretical analysis of the sodium diffusion in molybdenum thin films that lead to the measured SIMS data. It was observed that not only diffusion coefficients should be considered when analyzing diffusion processes in thin films but also the ratio of grain boundary size to grain size. Both depend on substrate temperature and directly affect the amount of diffused species in the film. The data were analyzed under the light of the film growth speed versus diffusion front speed, the effect of oxygen content, and the effect of substrate temperature on the overall diffusion process. The temperature inversely affects the ratio of grain boundary size and grain size and directly affects the diffusion coefficient, which leads to a preferable temperature at which the highest amount of alkali can be found in the film.