The aeronautical industry is looking with interest at friction-based welding for many years due to weight-saving capacities, where fusion-based welding problems can be avoided, allowing also the joining of materials considered complicated to weld with other technologies. Refill Friction Stir Spot Welding (refill FSSW) is a solid-state joining process that shows great potential to be a substitute for single-point joining processes like riveting. The main objective of this study is to investigate the mechanical behaviour of multi-spot joints of AA 2024-T3 obtained by refill FSSW with the addition of a sealant commonly used in riveted joints by the aviation industry. A fatigue test campaign was carried out on the joints with and without sealant to evaluate the possible synergy between the refill FSSW and sealant. The fatigue data obtained are statistically analyzed and compared. According to the comprehensive study including macro- and micro-structure, deformation strain field, residual stress distribution as well as the fatigue crack growth behaviour, the underlying history of multi-spot joints fatigue damage is revealed. The overall results prove that producing lap-joints by refill FSSW with sealant improves considerably the fatigue performance.