Friction stir welding (FSW) has been proposed as an alternative modern joining technology and demonstrated important benefits for the manufacturing of efficient and lightweight aircraft structures using high-strength aluminium alloys. These structures are required to be corrosion- resistant and thus, it is necessary to use technologies such as surface treatments and sealants in their manufacturing and assembly. In this work, the feasibility of combining innovative Cr-free surface treatments, sealants and FSW technology was investigated with the focus on the durability of the joints in fatigue. FSW lap joints were produced using AA2099-T83 extrusions and AA2060-T8E30 sheets in the as-received or surface-treated condition. A sealant was also applied in some cases at the overlapping interface before the FSW process. Static tensile tests and fatigue tests were carried out applying hoop-stress loading conditions. Different fracture modes were identified depending on the stress levels applied in the fatigue tests: High stress levels resulted in fractures in the HAZ of the FSW joints, while the specimens tested at low stress levels showed fractures out of the FSW joint. In general, FSW joints produced using surface-treated aluminium components and sealant presented improved fatigue life and extended durability in comparison with non-treated aluminium joints. The surface treatments and sealant at the interface of AA2099-T83 extrusions and AA2060-T8E30 sheets reduced the friction and local damage produced due to the sliding movement during the fatigue tests, minimizing the fretting fatigue effect, which was found to be the main limiting factor on the durability and fatigue life of the FSW joints.