Despite being a charter member of the newly-established Premier League, the club began a steady decline throughout the 1990s. Plans to build a new stadium in Merton came to nothing, and new Football Association guidelines released in the wake of the Taylor Report meant that staying at their home in Plough Lane was untenable. In an effort to control costs, the club entered into a groundshare agreement with South London rivals Crystal Palace, and began playing their home fixtures at Selhurst Park. Their form dropped precipitously, and despite some respectable runs in the FA Cup and League Cup they mostly finished in the middle and lower end of the table, with relegation being an ever-present threat.
At the turn of the millennium, a new business consortium sought once again to bring league football to Milton Keynes. Several clubs such as Luton and Queens Park Rangers were approached for a potential move, but none expressed any interest. But a new chairman at Wimbledon opened the door to talks, and in August 2001 the club formally stated their desire to relocate to the Buckinghamshire suburb. The move provoked widespread disapproval from fans and observers throughout the country, who feared the arrival of American-style franchising in the English game. The FA initially rejected the club’s application to move, insisting that the consortium establish a non-league club and earn a place in the Football League via promotion. The consortium, led by Pete Winkelman, appealed the decision, and the FA ultimately agreed to convene an independent commission to hear the case and offer a verdict. In May 2002, the independent commission voted 2-1 in favor of the club’s move to Milton Keynes, a decision widely condemned by fans of the club and the British sporting media.
The club played one last season at Selhurst Park to dwindling attendances before relocating to Milton Keynes in September 2003. At the end of the 2003-04 season, which they spent in administration, the club was relegated to the third tier of English football. When they began their League One campaign in August 2004, they bore the name Milton Keynes Dons. The South London club with over a century of history was, for all intents and purposes, dead.