It has been 11 years since a breakaway group of Manchester United supporters, weary of the commercialism and gluttony of the modern-day sport, and bitterly opposed to Malcolm Glazer’s takeover, set up their own club, and all those people who viewed them with cold, suspicious eyes, from Sir Alex Ferguson down, probably realise now that movement is here to stay.

Ferguson described FC United of Manchester as “sad” and stomped out of a press conference when he was asked if he had any words about the team’s first promotion under the management of Karl Marginson, a fruit-and-vegetable delivery man. Ferguson, rising from his seat, had four: “Not interested, not interested.”

Alan Gowling, a pundit on BBC Radio Manchester and former United forward, predicted the new club would not last until Christmas, a quote that is still celebrated on supporters’ T-shirts, and the idea of leaving one United for another will always divide opinion. You may recall the scene in Ken Loach’s film Looking for Eric when a supporter of each team is drinking in a pub and they become embroiled in a beery row about the rights and wrongs. “You can change your wife, your politics and your religion but never your football team,” the United fan says. It is followed by a killer line from the bloke in the non-sponsored FC shirt. “They left me,” he says.

Those arguments will probably continue until the year dot but they are used to it by now at Broadhurst Park, the £6.3m stadium that opened last May with the most vibrant atmosphere outside the four professional leagues and an old-school sense of belonging. “Pies not Prawns” read one banner in the early days. It felt real, exciting, progressive – united, in the true sense of the word, and very different to the Old Trafford culture of noodle partners, global tie-ups and a badge with the words “football club” lopped off.

FC United fans during the FA Cup qualifying first round match against Prescot Cables in 2014. Photograph: Chris Brunskill/Getty Images

Yet this season has been a strange one for FC. They are 12th in the National League North, having climbed to the sixth tier of the football pyramid, and attracted a crowd of 4,150 for last Saturday’s game against Chorley. There were 10 matches in League One and League Two watched by fewer people over the Easter weekend and when FC have that kind of pulling power it is tempting to think Manchester will eventually have a third representative among the 92 professional clubs.

And yet, behind the scenes, a club built on togetherness and shared principles has been undermined by the kind of infighting that could never have seemed imaginable. The general manager, Andy Walsh, announced last week he will stand down at the end of the season but that is only part of a story featuring legal action, resignations, protests, gagging orders and the overall feeling that FC are locked in an identity crisis.

The Guardian has seen correspondence from Tim Worrall, one board member, where he sums up the seriousness of it all. “The current divisions and rifts within the club represent a real business risk and need addressing urgently,” he says.

For Walsh, it is a galling way to end his time in charge. He has been an ambassador, spokesman and figurehead since the club’s early days but, equally, there is no doubt it is ending bitterly. One former board member quit the club a couple of weeks ago in protest about the way it is being run. A current board member is considering his position, disillusioned by the direction in which the club has been heading, and the split has led to an acrimonious dispute with John-Paul O’Neill, the man credited with setting up the club in 2005. O’Neill has persistently tried to tackle the board about what he sees as the abandonment of the club’s principles and has brought in lawyers because of alleged defamation.

Andy Walsh is standing down as the club’s general manager at the end of the season. Photograph: Christopher Thomond/The Guardian

Others are challenging the position of Andy Walker, an ally of Walsh’s, who goes by the title of fundraiser and communications officer and whose appointment has been described by Jonathan Kendal, formerly the chairman of the finance committee, as “greatly divisive”. A chant of “Walker out” was heard at the Chorley game and Kendal has emailed Worrall asking for an “urgent review” before a general meeting on 24 April. “The current divisions are extremely serious. It is a business risk for the club as a whole if the board do not examine the present divisive issues.”

All of this is happening at the same time as an internet poll shows 84% of supporters saying they have no confidence in the board appointing the right person as Walsh’s successor. For a club that always prided itself on being such a tight network, there is discord behind the scenes and it has filtered down to all levels. The programme editor, Tony Howard, an FC stalwart, resigned because of his frustrations with the board last June. Others have stayed away as a protest, or are threatening to. “There is a fundamental deficit in democracy, transparency and accountability between the club and its members,” O’Neill says. “After battling to expose it for months I’m no longer angry about it, just profoundly sad.”

It is a long, complex story, and not an easy subject to tackle when FC have been, and remain, a success story, frequently championed for their dedication to fans-owned clubs. Broadhurst Park has just been named the best new non-league stadium by the Football Grounds magazine, while Walsh and his colleagues have done an enormous amount of community work in the local Moston district. Walsh’s announcement about standing down referred to “a magnificent facility that I know our members are very proud of, and one that is the envy of many other clubs”. There have been four promotions in his time and he says he will remain involved in a different capacity.

It is also clear, however, that the split has become increasingly vitriolic and unpleasant. “The measure of a democratic organisation is how differing views are expressed, the nature of debate marks its character,” he said in a statement to the Guardian. “Debate and respect for others has always been part of FC United. Abuse and bullying are damaging and have no place at FC United as they threaten the very foundations on which the club’s success has been built.”

Others who are aligned to Walsh say the position is “horrific” because of the level of criticism, the growing divisions and the overall charge that the club has moved away from what it used to stand for. When the club that once boasted of “punk football” recently put out a code of conduct for consultation, giving supporters a long list of dos and don’ts, the crowd held up a banner adapted from a Pink Floyd song – “We don’t need no code of conduct, we don’t need no fan control” – and questions were asked about the reaction if the Glazers had done the same at Old Trafford.

Many members were also outraged that the club held a photoshoot with Damian Hinds, the exchequer secretary to the Treasury, during the Conservative party conference, despite a policy not to be used for political promotion and it being only a few days after a sizeable number of supporters marched against government cuts.

This season’s FA Cup first-round tie against Chesterfield was controversially moved to Monday to accommodate the demands of television. Photograph: Reuters

Like most clubs at their level, money is tight. FC are heavily reliant on fundraising and donations and have been running a £15,000 Kit out the Cabin appeal for the club’s academy players. Yet in February the board voted, 7-4, to hire Dave Boyle, formerly the chief executive at Supporters’ Direct, at a cost of £900 to look through the fans’ internet forums and report back on posts that could be described as harassment, unjustifiably abusive or potentially libellous from the previous nine months.

The irony is that Boyle has form himself for offensive use of social media, relinquishing his position at Supporters’ Direct in 2011 because of a series of abusive tweets that prompted the Premier League to temporarily withdraw its annual £1.2m funding. As if that were not awkward enough, he has also allegedly posted highly offensive comments on the When Saturday Comes message board about supporters from one FC forum.

His appointment smacks of “absolute bare-faced hypocrisy,” according to a recent blog on A Fine Lung, a website featuring a number of Manchester-based writers who have become increasingly critical of the FC regime. “Without a hint of irony, one of the leading lights of the supporter-ownership movement was offered a hefty sum of a supporter-owned football club’s money to snoop on the internet activity of co-owners of that very club, once the poster boys and girls of the supporter-ownership movement. This at a time when the club is struggling financially to adjust to the stresses and strains of owning our own ground.”

Fans’ banners at Broadhurst Park. Photograph: Nick Potts/PA ARCHIVE IMAGES

Boyle eventually pulled out, without being paid, and has told the Guardian it was a direct result of receiving a threatening anonymous phone call that he has reported to the police.

As for Howard, the dispute that led to his resignation had its origins in the club putting on a one-off 50p increase in ticket prices when they opened their new ground with a visit from Benfica last May. A small thing, you might think, but remember this is a club whose ethos was supposed to be against commercialism. Howard, a founder member, is said to have been “carpeted” when he made it clear he was against the increase and the people running the club have recommended Peter Thwaites, the voluntary HR official who puts contracts in place, inserts a confidentiality agreement for the new programme editor.

“I have drawn up dozens of contracts for club employees,” Thwaites responded in a post to the members’ forum. “Not one of these included a confidentiality or gagging clause, nor was it ever suggested that such a restriction was necessary. So why is there suddenly a need to invoke one for the programme editor? What state secrets are they ever going to be party to? Margy’s team selections?”

The post, subsequently deleted by the club’s moderators, added: “Let’s not kid ourselves here, this is nothing to do with confidentiality. This is the development of a systemic culture of secrecy, evasion and misrepresentation. Information is withheld, questions are not answered, restrictive codes of conduct are drawn up and attempts are made to stifle or silence criticism on the forums. Anyone who voices criticism of the way things are run is apparently viewed as an enemy of the club.”

Everything is likely to come to a head at the general meeting on 24 April and it will be a sorry way to end what has otherwise been a momentous season in their new home. “Publicity seekers,” Ferguson called them. It was never true – and this is one story they would rather did not have to be told.