Lyon could be banned from all European competition after Uefa on Monday charged the French club over incidents at last week's Europa League match against CSKA Moscow.
Uefa said the charges centre on racist behaviour and crowd disturbances. The club already have a suspended two-year ban hanging over them from incidents at a previous Europa League game with Turkish side Besiktas in April 2017.
Last Thursday's trouble started outside Parc OL, which will host the Europa League final in May, before the last-16 second leg against CSKA.
Police said that at least eight officers were hurt as 100-150 hooded fans attacked an anti-terrorist unit.
Problems continued inside the stadium and Uefa's Control, Ethics and Disciplinary Body has charged Lyon over the throwing of objects and the setting off of fireworks, crowd disturbances, racist behaviour and blocking stairways.
Lyon police said there were three arrests.
French sports daily L'Equipe quoted a source within Uefa as saying that the racism charge relates to Nazi symbols displayed inside the stadium, Nazi salutes and an attack on a non-white spectator.
CSKA won 3-2 on the night to progress to the quarter-finals on away goals, where they meet English club Arsenal.
The case will be decided on May 31. Under Uefa guidelines, the two-year suspended sentence will be automatically enforced if Lyon are found guilty.
Last April, at the quarter-final against Besiktas in Lyon, there were confrontations between the two sets of fans outside the stadium, fighting in the stands and a pitch invasion by dozens of Lyon supporters which forced the kick-off to be delayed by 45 minutes.
The latest incidents raise questions about security at the Europa League final on May 16, although Parc OL, built for Euro 2016, has already hosted several major matches with no notable incidents.
Marseille have also been charged by Uefa over "crowd disturbances" and "use of fireworks" in their home victory over Athletic Bilbao.