In the aftermath of the 2013 Egyptian coup d'état, El-Katatni was arrested on 4 July 2013. Egyptian prosecutor general Hisham Barakat ordered his assets to be frozen on 14 July 2013. On 29 October 2013, a three-judge panel at Cairo Criminal Court stepped down from the proceedings, citing "uneasiness" over the trial. On 11 December 2013, a second panel of judges withdrew from the trial. He was sentenced to life imprisonment in February 2015, a decision that was overturned in November 2016. As of September 2019, El-Katatni remains in custody pending retrial.