Al-Awlaki then moved to San Diego where he earned a Master's degree in Education Leadership at San Diego State University.  From 1996 to 2000, al-Awlaki also served as the imam at an Islamic center in San Diego, Masjid Ar-Ribat al-Islami. Two of the September 11 hijackers, Khalid al-Mihdhar and Nawaf al-Hazmi, attended prayers there in 2000, according to the 9/11 Commission Report. While in San Diego, Al-Awlaki also reportedly served as the vice president of the now-defunct Charitable Society for Social Welfare Inc., the U.S. branch of a Yemen-based charity that is still active today. In 2004, federal prosecutors in New York described the charity as a "front organization" that was "used to support Al Qaeda and Osama bin Laden," but the charity was never officially charged with a crime.

In January 2001, al-Awlaki moved to Falls Church, Virginia, where he began working on his doctorate in human resource development at George Washington University and served as the imam at Dar Al Hijrah mosque, one of the largest mosques in the U.S.  One of the September 11 hijackers who attended Awklaki's mosque in San Diego also attended Dar Al Hijrah with another September 11 hijacker, Hani Hanjour, according to the 9/11 Commission Report.

In an interview with al-Awlaki following the September 11 terrorist attacks, he admitted to meeting with al-Hazmi several times in San Diego, but claimed not to remember any specifics about their discussions and denied meeting with him or any of the other hijackers in Virginia, according to the 9/11 Commission Report.  Despite his denial, a congressional report states that the FBI had information that al-Awlaki "reportedly served as their spiritual advisor during their time in San Diego."

Nidal Malik Hasan, the alleged November 2009 Fort Hood gunman, reportedly saw al-Awlaki preach at Dar Al Hijrah mosque in Virginia in 2001 and 2002. 

Al-Awlaki publicly condemned the September 11 terrorist attacks, but also used them as an opportunity to criticize American foreign policy, especially regarding U.S. support for Israel. "Our hearts bleed for the attacks that targeted the World Trade Center as well as other institutions in the United States, despite our strong opposition to the American biased policy toward Israel" al-Awlaki said during a sermon at his mosque following the attacks. 

Al-Awlaki also spoke to reporters and members of his mosque about the difficulties Muslims are facing in the aftermath of the attack. He explained that while Muslim Americans are against terrorist attacks, they are "also against the killing of civilians in Afghanistan" and U.S. support for "the deaths and killing of thousands of Palestinians."

According to the 9/11 Commission Report, the FBI first began investigating al-Awlaki in 1999 and 2000, after learning of his possible connection to Al Qaeda. One of these connections was with Ziyad Khaleel, who authorities call a "procurement agent" for Osama bin Laden. Khaleel, who was the U.S.-based fundraiser for Islamic American Relief Agency – a U.S.-designated charity that listed itself as the partner of al-Awlaki's charity – may have visited al-Awlaki in San Diego, according to media reports.

Al-Awlaki reportedly moved to London in 2002 after FBI inquiries about his connection to September 11 hijackers, and then moved to Yemen in 2004.  In his audio recording released on March 17, 2010, al-Awlaki admitted that he left the U.S. after "the American invasion of Iraq and continued U.S. aggression against Muslims, I could not reconcile between living in the U.S. and being a Muslim."

Several months after he left the U.S., al-Awlaki returned for a brief visit with Ali al-Timimi, a U.S. citizen who frequently gave anti-Semitic, anti-Israel and anti-Western lectures at the Dar al-Arqam mosque in Falls Church, Virginia, and inspired a group of men dubbed the "Virginia Jihad Network" to attend Lashkar-e-Taiba terrorist training camps in Pakistan. Al-Timimi is now serving a life sentence for soliciting others to wage war against the U.S. and other related offenses. 

Before the visit with al-Timimi, al-Awlaki was detained at JFK airport in New York during his layover from Riyadh to Washington, D.C.  He was reportedly later released because a warrant for his arrest had been rescinded the day before.

Upon his return to Yemen, al-Awlaki worked at Iman University in Sanaa, according to the biography on his blog.  The founder and leader of the school, Shaykh Abd-al-Majid al-Zindani, was designated by the U.S. Treasury Department in 2004 as a Specially Designated Global Terrorist because of his support to Al Qaeda and Osama bin Laden.