The FA have also called on Chelsea manager Andre Villas-Boas to explain his blistering post-match tirade against referee Chris Foy and his assistants.
Chelsea's players have come under the disciplinary spotlight after several were seen to surround Foy following his controversial first-half dismissal of Jose Bosingwa at Loftus Road.
Villas-Boas later cited the incident as evidence of Foy's "card happy" performance, accusing the referee of failing to deal with both sides equally as Chelsea crashed to a 1-0 defeat.
"The FA has today charged Chelsea with failure to ensure their players conducted themselves in an orderly fashion," the FA said in a statement.
"This relates to an incident involving Chelsea players surrounding match official Chris Foy, immediately following Jose Bosingwa's dismissal.
"Separately, the FA has written to Chelsea manager Andre Villas-Boas and asked for an explanation on his post-match media comments.
"Villas-Boas has been asked to explain his comments on match official Chris Foy and the assistant referees.
"On both counts, the club has until Friday 28 October to respond."
Villas-Boas had stood by his remarks at a news conference on Tuesday shortly before the FA announced their charges.
"I don't think I said anything I shouldn't have," Villas-Boas said.
"I would never question the referee's integrity. But the fact is that, at the moment, we are paying heavily in terms of major decisions.
"Maybe this is what the FA (don't) want to hear from me - phrases like, 'The referee has influenced heavily three of our games'."