He was a German citizen, and was born to a Moroccan father and a German mother in 1975. The family moved to Morocco when he was nine years old. He came to Hamburg in 1995. He enrolled in an electrical engineering program at a technical university in 1996. He spent five months in the German army and then received a medical discharge. He lived in a student home during the weekdays and he spent weekends with his aunt, Barbara Arens. Both of them loved computers, and he called her his "high-tech aunt". She saw that he was secular until other students introduced him to radical Islam. She later put an end to the weekend visits. On November 1, 1998, he moved into an apartment in Germany with future hijackers Mohamed Atta and Ramzi bin al-Shibh. The Hamburg cell was born at this apartment. They met three or four times a week to discuss their anti-American feelings and plot possible attacks. Many al-Qaeda members lived in this apartment at various times, including hijacker Marwan al-Shehhi, Zakariya Essabar, and others. He served as the group's Internet expert. He had already been under investigation by German intelligence for his connections with Mohammed Haydar Zammar, a radical Islamic cleric. Through this, German intelligence was able to learn some of the activities of Atta and others, but the investigation was eventually dropped for lack of evidence. In October 1999, he got married at the Al-Quds Mosque in Hamburg. Atta, Jarrah, Shehhi, Zammar, and bin al-Shibh all attended his wedding. In late 1999, Atta, Shehhi, Jarrah, and bin al-Shibh decided to travel to Chechnya to fight against the Russians, but were convinced by Khalid al-Masri and Mohamedou Ould Slahi at the last minute to change their plans. They instead traveled to Afghanistan to meet with Osama bin Laden and train for terrorist attacks. There are conflicting reports as to whether he went with them; some news reports say that he went, but the 9/11 Commission Report says he stayed in Germany and helped cover for them in their absence. When the group returned to Germany, he was put on a border patrol watch list. He told his employer in June 2001 that he was going to an internship for a software company in Pakistan. His aunt, Barbara Arens, says that she was suspicious and that she went to the police and pleaded to them "to do something." She says that police took no action against him. Al-Qaeda leader Khalid Sheikh Mohammed told him in August that if he wanted to go to Afghanistan, he should go in the next few weeks, because it would soon become more difficult. He left Germany on September 4, 2001, just a week before the attacks, and flew to Karachi via Istanbul.
Aftermath of the attacks
He and cohort Ramzi bin al-Shibh were charged with 5,000 counts of murder by German officials. Bin al-Shibh was arrested on September 11, 2002, but Bahaji was still at large at the time. During the October 2009, Pakistan military operation against terrorists in South Waziristan, his German passport was found in a captured militant town.
Death
In August 2017, the Associated Press reported that al-Qaeda leader Ayman al-Zawahiri announced in an audio message that Bahaji had died but did not say when or how he died. In a list published by the United Nations Security Council of people and entities against whom there are sanctions, Bahaji is said to be "reportedly deceased in September 2013 in the Afghanistan/Pakistan border area."