In March 2013, Bassem Youssef started writing a weekly column expressing his views for Al-Shorouk; one of Egypt's most prominent and independent daily newspapers.
As Al-Bernameg continued with its growing success, Jon Stewart appeared as a guest on the show in June 2013.
On 1 July 2013 America in Arabic (United Arab Emirates) debuted. He appeared for the second time on The Daily Show with Jon Stewart.
After a four-month break, Youssef appeared on air in October 2013, with a show that stirred much controversy and criticism. In response to the popular criticism and discontent the show caused, CBC, the show's broadcaster, distanced itself from the show and its creators, and decided to stop airing it on its channels. Meanwhile, more than 30 complaints against Youssef and the show were filed at the General Prosecutor's office, accusing him of insulting the Egyptian Armed Forces and President Adly Mansour and describing the June 30 protests as a military coup, in addition to disrupting public order and peace. The General Prosecutor transferred some of the complaints for investigation, which were subject to the prosecutor's decision and judgment.
After a four-month break, Al Bernameg returned to air for its third series on 25 October 2013. The season premiere marked the first broadcast for the show since the 2013 Egyptian coup d'état had deposed Mohamed Morsi from the Egyptian presidency. Youssef criticised both the Morsi administration and the people's idolization of the Egyptian Defense Minister Abdul Fatah al-Sisi. The following day the CBC network issued a statement distancing the channel from the political stance taken by Youssef. The CBC network issued another statement, and decided to stop broadcasting Al Bernameg because of violations in the contract signed.
On 1 January 2013, the daily Al-masry Al-youm reported that an Egyptian prosecutor was investigating Bassem Youssef on charges of maligning President Mohammed Morsi, whose office claimed that Youssef's show was "circulating false news likely to disturb public peace and public security and affect the administration."
On 30 March 2013, an arrest warrant was issued for Youssef for allegedly insulting Islam and Morsi. The move was seen by opponents as part of an effort to silence dissent against Morsi's government. Youssef confirmed the arrest warrant on his Twitter account and said he would hand himself in to the prosecutor's office, jokingly adding, "Unless they kindly send a police van today and save me the transportation hassle." The following day, he was questioned by authorities before being released on bail of 15,000 Egyptian pounds. The event sparked international media attention as well as a segment on Jon Stewart's The Daily Show in which he declared his support for Youssef, calling him a "friend" and "brother".
In 2013, Youssef was named one of the "100 most influential people in the world" by TIME magazine and one of Foreign Policy magazine's 100 Leading Global Thinkers.
In November 2013, Youssef's role in the media was recognized by the Committee to Protect Journalists, which awarded him with the International Press Freedom Award, along with three other journalists.