Clattenburg has been accused of using 'inappropriate language' towards Blues players - believed to be Juan Mata and John Obi Mikel - during their eventual 3-2 loss to Manchester United at Stamford Bridge on Sunday.
The FA were already investigating the incident, as are the Metropolitan Police, and now the Blues have lodged an official complaint to keep the ball rolling.
"Following Sunday's Premier League game against Manchester United, club board members were quickly made aware, upon entering the home dressing room after the final whistle, that there were allegations of inappropriate language directed at Chelsea FC players by Mr Clattenburg during the game," read a Chelsea statement.
"Board members began establishing the details of the allegations, speaking to all relevant players and staff. After those initial interviews, it was clear that the matter had to be reported.
"The correct protocol for doing so was to report the incidents to the match delegate, and the club took immediate steps to inform him as soon as he was available. It was not a decision the club took lightly.
"Since reporting the matter to the delegate, the club and outside legal counsel have conducted further investigations.
"Having completed that process, we have now followed the correct protocol and lodged a formal complaint with The FA regarding John Mikel Obi.
"There was not sufficient evidence to support a second claim to the FA with regard to the alleged verbal abuse of another first-team player."
In addition, Clattenburg has been stood down from officiating matches this weekend as he attempts to clear his name.