Since their promotion to the top division they have not been relegated, and won their first title in 2012. This qualified the club to the 2012–13 UEFA Champions League, where they were knocked out 9-1 on aggregate in the first qualifying round by Maltese champions Valletta. They won their second league title in 2013, this qualified the club to the 2013–14 UEFA Champions League they were drawn to play EB/Streymur of the Faroe Islands, in the first leg they drew 2–2 despite winning 2–0 and missing a penalty to go 3–0, in the second leg they lost 5–1, losing 7–3 on aggregate.
FC Lusitanos' logo greatly resembles that of the Portuguese Football Federation. Since its founding, the club has had several Portuguese players, coaches and supporters (mainly Portuguese immigrants in Andorra). The team's kit manufacturer is the Portuguese brand Peba.