During the Gulf War he was an eyewitness to the bodies being removed from the Al Amiriyan air raid shelter in Baghdad, where hundreds of civilians had been killed.

He was also a guest host on the satirical panel game Have I Got News for You, and presented the BBC's 2001 three-part series Son of God, an investigation into the life of Jesus.

[4] Nonetheless, he returned to the field in March 2003 as a special correspondent,[14] during which time he covered the death of Pope John Paul II.

[20] The complaints included 24 allegations of breaching BBC guidelines on accuracy and impartiality, of which three were fully or partially upheld.

[23] The BBC Trust accepted that for a claim that was found to be lacking in accuracy that Bowen had been provided with the information by an authoritative source.

[22] In February 2011, Bowen became the first British journalist to interview Muammar Gaddafi since the start of the 2011 Libyan civil war against him and the government.

One of these notebooks was subsequently found in the remains of a military convoy, which the rebel force that attacked it said contained Gaddafi's son, Khamis.

The notebook contained both Bowen's words and a number of notes in Arabic detailing military manoeuvres and a list of persons to be detained.

[26][27] On 5 July 2013, Bowen was reporting for the BBC on the protests in Egypt regarding the former President Morsi when he was shot in the head with shotgun pellets.

Bowen was the editor responsible for overseeing this coverage, and has been criticised for the BBC's inaccurate reporting on the incident for repeatedly implying that Israel bombed the hospital, destroyed the facility, and killed 500 people.