[3] In December 2011, the second edition of the newspaper was prevented from being printed, following internal censorship of an article[4] written by political scientist Robert Springborg which was critical of the Supreme Council of the Armed Forces.

[6] The editorial team decided to put together a closing edition, which would have been published on 25 April, "to explain the conditions under which a strong voice of independent and progressive journalism in Egypt is being terminated".

[12] In July 2013, an article by the Associated Press about media bias in Egypt following the overthrow of Mohamed Morsi quoted Lina Atallah, editor-in-chief of Mada Masr, as saying that there was increased pressure on journalists to toe the line, pointing to the coverage of protester killings, which repeated the interim government and military's official narrative.

[13] Mada Masr has been blocked in Egypt since May 2017, alongside twenty other websites featuring political content perceived as friendly to the Muslim Brotherhood and hostile to the government.,[14] and dissident contributing writers.

Lawyers representing Mada Masr and the Communications and Information Technology Ministry argued that the NTRA was solely responsible, and the NTRA countered that website blocks fell under the purview of the Supreme Media Regulatory Council or a national security body, which includes the presidency, the Interior Ministry, the General Intelligence Services and the Administrative Control Authority, as designated by Article 1 of the communication law (Law 10/2003).

According to Article 64 of the law, the Armed Forces are also considered an agency concerned with national security, when it comes to technical capabilities that include telecommunications equipment, systems and programs.

[15] On 24 November 2019, plainclothes police officers raided the headquarters of Mada Masr, briefly arresting Atallah as well as staff members Mohamed Hamma and Rana Mamdouh.

The Egyptian prosecution, citing national security investigations, alleged that Mada Masr was founded by the illegal Islamist organization the Muslim Brotherhood, with the intent of spreading fake news.

[20] On 8 September 2022, Egyptian authorities summoned and interrogated Mada Masr Editor-in-Chief Lina Attalah and journalists Rana Mamdouh, Sara Seif Eddin, and Beesan Kassab.