Due to its high productivity, low cost, and increased work efficiency, resistance spot welding (RSW) can instantly join two or more steel sheets and it is widely used in the automotive industry and lately in the manufacturing of thin-walled cold-formed steel constructions. However, the RSW of zinc-coated mild steel sheets presents metallurgical challenges, especially when different thickness combinations are used. Therefore, in the present paper a resistance welding machine was used which uses direct current (MFDC) inverter technology combined with SMART AUTOSET technology to weld S250 GD and S350 GD galvanised mild steel sheets with different thicknesses. It is well known that, due to the elevated temperature that occurs during the welding process, followed by rapid cooling, defects such as cracking, porosity, lack of fusion, and an increased amount of brittle phases affect the welding quality. Therefore, the influence of the RSW process parameters established by an automatic sequence on the nugget geometry, microstructure, and mechanical properties was investigated. The phase transformations that took place during the heating-cooling cycle were analysed in detail through metallographic studies. The results showed that the microstructure of the weld nuggets was similar, characterised by columnar grains elongated in the direction of heat evacuation. Nevertheless, there were differences in terms of phase dispersion, defects and mechanical properties that have been linked to the RSW process parameters.