In 2000, journalist Mona Chollet was sacked after she had protested against a Philippe Val article which called Palestinians "non-civilized"
. In 2004, following the death of Gébé, Val succeeded him as director of the publication, while still holding his position as editor.
Controversy arose over the publication's edition of 9 February 2006
. Under the title "Mahomet débordé par les intégristes" ("Muhammad overwhelmed by fundamentalists"), the front page showed a cartoon of a weeping Prophet Muhammad saying "C'est dur d'être aimé par des cons" ("it's hard being loved by jerks"). The newspaper reprinted the twelve cartoons of the Jyllands-Posten Muhammad cartoons controversy and added some of their own
. Compared to a regular circulation of 100,000 sold copies, this edition enjoyed great commercial success. 160,000 copies were sold and another 150,000 were in print later that day.
In 2008, controversy broke over a column by veteran cartoonist Siné which led to accusations of antisemitism and Siné's sacking by Val. Siné sued the newspaper for unfair dismissal and Charlie Hebdo was sentenced to pay him €90,000 in damages.
 Siné launched a rival paper called Siné Hebdo which later became Siné Mensuel. Charlie Hebdo launched its Internet site, after years of reluctance from Val.
In 2009, Philippe Val resigned
after being appointed director of France Inter, a public radio station to which he has contributed since the early 1990s. His functions were split between two cartoonists, Charb (Stéphane Charbonnier) and Riss (Laurent Sourisseau)
. Val gave away his shares in 2011.