His family had no knowledge of his whereabouts for 10 days after his arrest. He was held in an unknown location for a week before being transferred to section 209 of Tehran’s Evin prison, where he was held for seven months, three of them in solitary confinement. He has since said that, while in solitary confinement, he was denied access to a lawyer and was forced to make “confessions” in front of a video camera by reading out statements pre-written by his interrogators. He has said that he was put under intense pressure through torture and other ill-treatment, including threats to execute him, his children who live in Sweden, and his elderly mother who lives in Iran, to “confess” to being a spy. He denies the accusations against him and says they have been fabricated by the authorities. In an August 2017 letter written from inside Evin prison, he says he was asked by the Iranian authorities in 2014 to “cooperate with them to identify and gather intelligence from EU states…My answer was ‘no’ and I told them that I am just a scientist, not a spy.”
On 24 October 2017, during his weekly press conference with journalists, the Prosecutor General of Tehran, Abbas Ja’fari Dolat Abadi said, without specifically naming Ahmadreza Djalali, that “the defendant” had held several meetings with [Israeli intelligence agency] Mossad and provided them with sensitive information about Iran’s military and nuclear sites in return for money and residency in Sweden.