Ajax is facing a fourth UEFA punishment this season for fan misconduct at Champions League games.
UEFA says Ajax has been charged with fans throwing objects and "acts of damage" at Real Madrid's Santiago Bernabeu Stadium in a 4-1 victory last week.
UEFA's disciplinary panel will judge the case on March 28, ahead of the quarterfinals.
Ajax has been ordered to pay a total of 77,000 euros ($87,000) for crowd disturbances and other incidents at three games earlier in the competition.
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After a group game at Benfica, UEFA put Ajax on probation for one year with a threat to ban selling tickets to fans for an away game.