Friction stir welding (FSW) has emerged as an advanced solid-state joining process for aluminum alloys, offering significant advantages over conventional fusion welding techniques. The process produces different microstructural regions, namely the nugget zone, thermo-mechanically affected zone, heat-affected zone, and base metal, each exhibiting unique thermal histories and material characteristics that govern the final joint performance. Continuous research efforts have led to the development of several FSW variants and process modifications aimed at improving joint quality, microstructural homogeneity, and service performance. Among these developments, stationary shoulder friction stir welding has attracted considerable attention due to its ability to reduce heat input, minimize heat-affected zone width, and produce smoother, more symmetrical welds. This chapter provides a comprehensive overview of the influence of process parameters, tool geometry, pre- and post-weld heat treatments, post-weld surface treatments, external particle reinforcement, and cooling conditions on the microstructure and mechanical properties of friction stir welded aluminum alloys. The discussion highlights recent advancements and the underlying mechanisms governing microstructural evolution and property enhancement, providing valuable insights for optimizing FSW processes for high-performance engineering applications.