Bury have been ordered to play two home games behind closed doors for offensive comments made by supporters during a match at Gigg Lane.
The punishment, and a £350 fine, were imposed following the incidents at a North West Counties Premier Division game with West Didsbury & Chorlton.
The charge related to alleged racist and homophobic language and behaviour.
Bury said in a statement that they intend to appeal against the “excessive” punishment.
The Shakers, who said they “accepted the facts of the incident”, claimed that the comments were only made by two fans at the game in September.
However, in their written reasons, the Manchester Football Association said seven previous “serious misconduct findings” involving the club’s supporters had contributed to the punishment.
“We accept there should be a punishment, but excluding every well-behaved football supporter from a stadium which has already excluded those who perpetrated the offences, does nothing to promote inclusion,” the club said.
“The loss of revenue is extremely damaging and our belief is that it would be far better to use that revenue to fund a campaign intended to positively promote diversity and inclusion.”
Bury, who are second in the table, are set to face leaders Wythenshawe behind closed doors on 16 January and Ramsbottom United a week later.
A report from Kick It Out, that was given to the Manchester FA, said that a Bury supporter at the game against West Didsbury & Chorlton used a homophobic term when shouting at an away supporter, as well as another racial slur towards another person.
Homophobic gestures were also alleged to have been used, while further offensive language was directed towards supporters using disabled facilities at Gigg Lane.
“Sadly, for Bury FC, the poor behaviour has now escalated into a further finding of abusive behaviour that included discriminatory references,” the Manchester FA statement said.
“The commission chair was left with no choice but to substantially increase the seriousness of the sanction passed against the club.”
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