This work focuses on the microstructural characterization of aluminum to steel friction stir welded joints. Lap weld configuration coupled with scribe technology used for the weld tool have produced joints of adequate quality, despite the significant differences in hardness and melting temperatures of the alloys. Common to friction stir processes, especially those of dissimilar alloys, are microstructural gradients including grain size, crystallographic texture, and precipitation of intermetallic compounds. Because of the significant influence that intermetallic compound formation has on mechanical and ballistic behavior, the characterization of the specific intermetallic phases and the degree to which they are formed in the weld microstructure is critical to predicting weld performance. This study used electron backscatter diffraction, energy dispersive spectroscopy, scanning electron microscopy, and Vickers micro-hardness indentation to explore and characterize the microstructures of lap friction stir welds between an applique 6061-T6 aluminum armor plate alloy and a RHA homogeneous armor plate steel alloy. Macroscopic defects such as micro-cracks were observed in the cross-sectional samples, and binary intermetallic compound layers were found to exist at the aluminum-steel interfaces of the steel particles stirred into the aluminum weld matrix and across the interfaces of the weld joints. Energy dispersive spectroscopy chemical analysis identified the intermetallic layer as monoclinic Al3Fe. Dramatic decreases in grain size in the thermo-mechanically affected zones and weld zones that evidenced grain refinement through plastic deformation and recrystallization. Crystallographic grain orientation and texture were examined using electron backscatter diffraction. Striated regions in the orientations of the aluminum alloy were determined to be the result of the severe deformation induced by the complex weld tool geometry. Many of the textures observed in the weld zone and thermo-mechanically affected zones exhibited shear texture components; however, there were many textures that deviated from ideal simple shear. Factors affecting the microstructure which are characteristic of the friction stir welding process, such as post-recrystallization deformation and complex deformation induced by tool geometry were discussed as causes for deviation from simple shear textures.