The present study investigated a new configuration of friction stir welded joints from two aluminum alloys. Dissimilar welds AA6082/AA1350 were examined, whereas, for AA1350, two states were investigated—coarse-grained (CG) and ultrafine-grained (UFG). Changes in the mechanical and electrochemical properties regarding the microstructure evolution across the welds were discussed. The average grain size in the stir zone (SZ) for all materials equaled 4 to 5 µm with a fraction of high-angle grain boundaries of about 77 pct, indicating the occurrence of continuous dynamic recrystallization. Changes in the microhardness across the welds were connected with differences in grain size (AA1350) and dissolution of β″ precipitates in the SZ of AA6082. As a result, the tensile strength of the welds decreased compared to base materials AA6082 and AA1350 UFG; however, there was an increase when compared to the base material AA1350 CG. Electrochemical experiments revealed that pitting corrosion occurred for AA1350, while for AA6082, it was a combination of pitting and intergranular corrosion. The depth of corrosion attack was higher for AA1350, with a maximum value of ~ 70 µm for base materials, while in the SZ, a depth decreased to 50 µm. For the AA6082, the maximum depth was measured in the SZ and did not exceed 30 µm.