Coleman criticised the performance of referee Steve Bennett after his team's 2-0 defeat to the Premier League giants at the Ricoh Arena on March 7, labelling the Kent official "smug".
And the FA have now decided to charge the Welshman with improper conduct and/or bringing the game into disrepute following his comments to the media.
Coleman has been given until April 2 to respond to the charge.
He also said after the clash: "I was disappointed with Mr Bennett all
afternoon as were my players - his attitude towards us and towards them.
"I know it was Chelsea who are a great team who deserve respect and he let us know that in no uncertain terms.
"That is not why we lost but I was disappointed with that. He was smug towards us, the way he was talking to my players, my senior players.
"He was very friendly towards some of the Chelsea players. I know they are great players but you are there to do a job and my players are not happy with his attitude.
"Then for the second goal Chelsea had two players off the pitch for treatment. You are not supposed to wave them back on until you see where the ball is going to bounce and so they gain no advantage.
"You can't wave them back on in a situation like that and who scores the goal - Alex."