Murton became Second Division champions. In Murton's first season in the First Division they finished 13th out of 20 teams but in the second season Murton once again improved by finishing runner up on goal difference to Gretna. In the 1992-93 season Murton won the top cup competition in County Durham by winning the Durham Challenge Cup after beating Northern Premier League team Bishop Auckland. That was the last success Murton had, the money eventually ran out and Murton suffered relegation in 1997-98 having conceded 170 goals and scored only 20. A decision was made to resign the club from the league unless more committee members were prepared to come along and help. People did come on board and the club survived, then in the summer of 2000 a hole appeared in the pitch overnight. A collapsed culvert had caused water to erode the soil underneath the pitch causing part of the pitch to collapse in on itself. The pitch was eventually repaired thanks to a grant from the Football Foundation and Murton returned home in October 2001 after playing their home games at Peterlee Town and Kennek Ryhope Community Association (now known as Sunderland Ryhope Community Association). In 2004 the club was expelled from the Northern League as its facilities were deemed not up to standard. Murton joined the Northern Alliance Premier Division for the following season but were relegated in the 2005–06 season. On 11 April 2007 they played in their first cup final since winning the Durham Challenge Cup in the 1992–93 season. They took on Gillford Park from Carlisle and after conceding a late first half goal lost the final 1-0. On 21 April 2008 Murton won the Durham FA Trophy for the first time in their history defeating Whitehill Welfare of the Durham Alliance 3-1. This was also their debut in the competition, previously competing the Durham FA Challenge Cup. They subsequently gained promotion to the Premier Division finishing as runners up in the First Division. The 2008–09 season saw the club struggle again in the Premier Division and towards the end of the season, manager Brian Maxwell resigned. He was replaced by senior players Andrew Upperton and Stephen Turner who were at the time joint managers of Murton Victoria in the Peterlee & District Sunday League. Relegation was avoided by virtue of the decision by the Northern Alliance committee to only relegate the bottom