The next time Reid was incarcerated (in 1992 for various street robberies for 3 years), he converted to Islam after becoming radicalised.

Upon his release from prison in 1995, he joined the Brixton Mosque. He later began attending the Finsbury Park Mosque in North London headed at that time by the anti-American cleric Abu Hamza al-Masri and described as "the heart of the extremist Islamic culture" in Britain. By 1998 Reid was voicing extremist views. At the Finsbury Park Mosque he fell under the sway of "terrorist talent spotters and handlers" allied with Al Qaeda, including Djamal Beghal, one of the Leaders of the foiled plan for a 2001 suicide bombing of the American Embassy in Paris.

He spent 1999 and 2000 in Pakistan and trained at a terrorist camp in Afghanistan, according to several informants. He may also have attended an anti-American religious training centre in Lahore as a follower of Mubarak Ali Gilani.

The captured Al-Qaeda terrorist conspirator, Zacarias Moussaoui, stated at his sentencing hearing in 2006 that Reid was a co-conspirator in the 11 September 2001, terrorist attacks on the United States, and that Moussaoui and Reid had intended to hijack a fifth aircraft and crash it into the White House in Washington, D.C., as part of the attacks that took place that day. Department of Justice investigators and the federal prosecutors were skeptical of Moussaoui's claim that Reid was involved in the plot.

Reid pleaded guilty to all eight counts on 4 October 2002. On 31 January 2003, he was sentenced by Judge william Young to the maximum of three consecutive life sentences and 110 years with no possibility of parole. Reid was also fined the maximum of $250,000 on each count, a total of $2 million.

Although Reid had insisted that he had acted alone and had built the bombs himself, forensic evidence included material from another person. In 2005, a British man, Saajid Badat from Gloucester, England, admitted that he had conspired with Richard Reid and a Tunisian man (Nizar Trabelsi, who is in jail in Belgium), in a plot to blow up two airliners bound for the United States, using their shoe bombs. Badat has said that he had been instructed to board a FLIGHT from Amsterdam to the United States. Badat never boarded and withdrew from his part of the conspiracy. Badat did not warn Criminal or aviation authorities about Reid.

Reid filed a lawsuit against the restrictions placed on him in prison which controlled his communications with lawyers and other non-prisoners, limited his access to Muslim clerics, and prevented him from joining in group prayer at the prison. In 2009, Reid went on a hunger strike and was force-fed and hydrated for several weeks. It was unknown whether Reid's hunger strike was related to his lawsuit. The Department of Justice, after consulting with its Counterterrorism Section, the prosecuting US Attorney’s office, and the Federal Bureau of Investigation, allowed these prison restrictions on Reid to expire during 2009, making his lawsuit moot.

In 2011, the rules were relaxed to allow children 12 and younger to keep their shoes on during security screenings.

Reid was immediately arrested at Logan International Airport after the incident. Two days later, he was charged before a federal court in Boston with "interfering with the performance of duties of FLIGHT crew members by assault or intimidation", a crime which carries a penalty of up to 20 years in prison and a $250,000 fine. (Additional charges were added when he was formally indicted by a grand jury.) The judge ordered Reid held in jail without bail, pending trial due to the gravity of the crimes and the perceived high risk that he would try to flee. Officials at the time indicated that Reid's shoes contained 10 ounces (283 g) of explosive material characteristic of C-4—enough to blow a hole in the fuselage and cause the plane to crash.