The joining of aluminum alloy AA5052 and carbon-fiber-reinforced polyether ether ketone (CF/PEEK) by friction lap welding was investigated under different conditions of surface texturing and process temperatures. The joint quality was evaluated by measurement of the tensile shear force and examination of the joint morphology. The aluminum alloy underwent two different types of surface texturing—mechanical engraving and sandblasting. The welding experiments were then conducted under different tool rotational speeds for each. The temperatures across the weld line were measured during the welding process using thermocouples mounted at specific locations. The temperature distribution at the interface was determined by an inverse heat conduction method. It was found that the temperatures at the interface exceeded the melting temperature of PEEK for all testing conditions but was always below PEEK thermal degradation temperature. It was also found that joint performance of mechanically engraved samples increased with the increase of interface temperatures. This was attributed to the increased mechanical interlocking due to the flow of melted PEEK into the engraved sample’s surface features. The joint strength of sandblasted samples did not change considerably with interface temperatures.