Laser micro-welding differs from macro-welding in that at least one dimension of the weld is less than 100 μm. Although process research on laser micro-welding has recently made some progress, the influence of welding mode on microstructure and corrosion resistance has remained unknown, which has been shown to have a significant influence on laser macro-welding. In this work, a single-mode fiber laser equipped with a scanning galvanometer is used to weld AISI304 stainless steel foils with a thickness of 100 μm. Similar to laser macro-welding, keyhole formation is used to describe two welding modes, namely thermal conduction welding and penetration welding. The laser-material interaction experiences a transient phase in which the welding mode alternates between conduction welding and penetration welding as reported by previous work. However, we show that gas protection eliminates the transient phase, proving that the transient phase develops as a result of the unsteadiness of the penetration welding caused by oxidation during the welding process. The crystallographic texture and phase constitution vary between conduction and penetration welds due to variations in heat transfer behavior during welding. The conduction weld has greater Σ3 CSL boundaries and a more uniform microstructure than the penetration weld, resulting in better corrosion resistance.