He will receive an automatic four-match ban as it was his second dismissal of the season, and could receive three-match suspensions for each of the violent conduct charges.
On top of that, the FA's regulatory panel will have discretionary powers to increase the length of the suspension if charges are found to be proven.
That leaves the midfielder facing a lengthy suspension at the start of next season - something that could deter interest from other clubs in signing him if QPR decide they wish to part company.
Barton insisted via Twitter that he had not lost his head but that a team-mate "suggested I should try to take 1 of theirs with me".
QPR chairman Tony Fernandes said Barton's future would be reviewed but that the 29-year-old had been an integral part of the club.
"There are experienced people who will come back to me and we'll review the whole situation," he told BBC Sport.
Fernandes highlighted the fact that Djibril Cisse was also sent off twice since in January.
He added: "Joey has been an integral part of the club and has played his part. Cisse has been sent off twice, and I think he was critical for us in terms of getting goals.
"This is football, and I'm new to it. I don't profess to have all the answers."
Barton denied trying to deflect attention away from his behaviour after launching an expletive-laden attack on Alan Shearer, his former manager at Newcastle and current Match of the Day pundit.
Barton said on Twitter: "No deflections here mate. Think the fact about 100m people seen it will see to that. Just don't like how he goes personal...''
He added: "Right enough about yesterday [Sunday], I apologise to everyone offended by it. If that's not enough for some, so be it. Life is too short.
"Things happen on the pitch, in the heat of battle sometimes. Not how we always plan them to happen.
"Still don't think it is a sending off. The head was never gone at any stage. Once I'd been sent off, one of our players suggested I should try to take 1 of theirs with me. Never worked but god loves a trier.
"Think a few people are forgetting Tevez started the fracas by throwing a punch to the head."
Watch: Barton charged over City sending off... More Videos
Barton has until 6pm on Tuesday to respond to the charges.
The FA said in a statement: "The FA has today [Monday] charged Queens Park Rangers midfielder Joey Barton in relation to two acts of alleged violent conduct during Sunday's match against Manchester City at the Etihad Stadium.
"Following the player's dismissal in the 54th minute of the fixture, there followed two incidents involving Manchester City's Sergio Aguero and Vincent Kompany.
"As Barton had already been dismissed, both of these incidents fell outside of the jurisdiction of the referee."