Success then was harder to come by, and by 2002 the club's future was in grave danger and they had quit the Hellenic Football League at the end of the 2002–03 season.
The club had tried to improve its facilities for many years; in 1994 their basic railed-off pitch had denied them the chance of promotion to the Isthmian League Premier Division.
The club briefly played in the FA Vase in the mid-1990s: 1993–94 Reached 1st Qualifying Round and beat Oxford City F.C.
1994–95 Knocked out in the Extra Preliminary Qualifying Round 1–2 to Flight Refuelling F.C -(now known as Merley Cobham Sports F.C.).
Peppard F.C also entered a team in the FA Sunday Cup for one season in 1998–99, which has since merged with Theale F.C.