On 27 July 2019, he was arrested by Jammu and Kashmir police and held in custody at Saddar police station in Anantnag district. He was questioned about his article and subsequent ones[11] on the deployment of new Indian troops in the region.[12] Shibli was detained under the recently published Public Safety Act, which allowed the arrest of people older than sixteen years old for a period of two years.[13] On 5 August, when a media shutdown in Jammu and Kashmir was imposed as a consequence of the abrogation of constitutional provisions granting special autonomy to Jammu and Kashmir, his family lost contact with Shibli. They only learned of his whereabouts only after more than 2 months in custody, when he had already been transferred to a prison in Uttar Pradesh. It was later revealed that Shibli was charged with accusations including "waging war against the Union of India," "creating fear and panic among common people," being "deeply involved in disrupting the peaceful atmosphere," and seeking "to motivate the people to work for seceding the state of Jammu and Kashmir from the union of India" on 8 August, leading to charges of pro-independence activity. On 9 August he was transferred to Bareilly District Prison in Uttar Pradesh, 1,300 km from his hometown.[12] In December, Time reported on his case as one of the "10 Most Urgent Press Freedom Threats".[1] The Committee to Protect Journalists, an international organization that defends journalists' rights, also reported on Shibli's arrest and campaigned online for the charges against him to be dropped. On 13 April 2020, he was released from prison and went back to his hometown of Anantnag in Kashmir.[11]
On 30 July 2020, he was summoned by Jammu and Kashmir Cyber Police to appear the next day at Srinagar Police Station.[14] On 31 July 2020, he was transferred to Shergarh Police Station.[15] On 2 August 2020, people from across the world and from different backgrounds took to Twitter to condemn Shibli's detention.[15] On 3 August 2020, he was transferred to Srinagar Central Prison. He has been booked under 107 CRPC, a section for Security for keeping the peace in other cases.[16] After eighteen days, on 17 August, he was released.[17]
On August 05, 2020, his house was raided for several hours and several gadgets were confiscated.[18] The houses of his close relatives who live in the same town were also raided, as per CPJ.
In November 2022, his house was raided again by the State Investigating Agency of the Police.[19]