League reorganisation saw Molsely placed in Division Two South in 1984, where they remained until finishing as runners-up in 1989–90, earning promotion to Division One. They won the Southern Combination Challenge Cup in 1990–91. In 1992–93 the club were Division One runners-up and were promoted to the Premier Division. The 1993–94 season saw them reach the first round of the FA Cup for the first time, losing 4–0 at home to Bath City; the club also won the Southern Combination Challenge Cup for a second time. They were relegated back to Division One at the end of the 1995–96 season and then to Division Two in 1998–99. Further league reorganisation in 2002 led to the club becoming members of Division One South, before being placed in Division One in 2004 and then back in Division One South in 2006 as the league was restructured.