Considered a political prisoner, Khalid has been imprisoned in Tihar Jail for alleged involvement in the 2020 Delhi Riots since September 2020 and has consistently been denied bail, even though his court trial is yet to begin.

[16][17][18] Khalid's PhD thesis was titled “Contesting claims and contingencies of the rule on Adivasis of Jharkhand” and was submitted to the JNU in 2018.

[19] Following his PhD, he published a research article titled "Changing Village Authority in an Adivasi Hinterland: State, Community and Contingencies of Rule in Singhbhum, 1830–1897" in the journal Social Scientist in 2018.

[20] On 9 February 2016, students of JNU held a protest on their campus against the capital punishment meted out to the 2001 Indian Parliament attack convict Afzal Guru and Kashmiri separatist Maqbool Bhat.

[21] Four days after the event, the Delhi Police arrested JNU Students Union (JNUSU) president Kanhaiya Kumar on charges of sedition and criminal conspiracy.

Speaking to The Hindu, Khalid said the administration had not filed a police complaint regarding the incident (and only the family and students had) and have not taken action against those who attacked Najeeb.

[36] On 15 October 2019, United Against Hate (a campaign group) organised a protest march at Jantar Mantar, New Delhi to mark three years of the disappearance of Najeeb.

Khalid expressed his solidarity and joined the march alleging that the fact that investigative agencies including the CBI have not made any progress showed that there have been no efforts to find Najeeb, while his attackers were being protected.

Before the arrest, the accused had uploaded a video on Facebook on 15 August, saying the attack was an Independence Day gift for India, and they also wanted to highlight the issue of cow protection.

[42][43] Umar Khalid was booked under UAPA by Delhi Police for his alleged "provocative speeches" during the visit of American President Donald Trump to India.

[48][49] In charge sheets related to the riots, the police have said Khalid met suspended and jailed Aam Aadmi Party's councillor Tahir Hussain and activist Khalid Saifi on 8 January at the Shaheen Bagh sit-in protest site against the Citizenship (Amendment) Act (CAA)-National Register of Citizens (NRC) to allegedly plan the riots.

In the bail order the court said that the allegations against Khalid are prima facie true and his role in the "context of conspiracy" related to Delhi riots was apparent.

[61][62] As of October 2024, Khalid had been jailed for four years without a trial, prompting the New York Times to describe him as "a symbol of the wide-ranging suppression of dissent under Prime Minister Narendra Modi.