Uefa laid the charges following incidents outside Lyon’s Groupama Stadium ahead of the club’s Europa League match against CSKA Moscow on Thursday.
Police say up to 150 Lyon "ultras" attacked officers, injuring eight of them.
Other charges include throwing objects, setting off fireworks and blocking stairways.
The club condemned the incidents as “intolerable and premeditated attacks”.
It already has a suspended two-year ban hanging over it from incidents at a game against Turkish side Besiktas in April 2017.
Uefa rules state that suspended bans must be enforced if further offences are committed during probation periods.
The club could face a one-season ban from Uefa competitions.
The governing body will deal with the case on 31 May.