Founder, Lisa McPherson trust
Minton became a critic of Scientology after reading about its attacks on critics and internet free speech. He appeared on several news programs discussing his criticism of Scientology and the harassment from the church. This included a feature appearance on the June 16, 1998 broadcast of the television news program Dateline NBC. Later that year, he appeared in an A&E "Investigative Reports" installment called "Inside Scientology" which aired in December.
Minton spent over $10 million fighting Scientology. He also participated in demonstrations in front of the Boston Headquarters of the Church of Scientology near his Beacon Hill home.
After reports by Scientology alleging fraud in his Nigerian businesses, Minton successfully sued two German Scientology entities and a spokeswoman for a permanent injunction preventing them from repeating the libel. The decision was confirmed on appeal.
Minton was the founder of the Lisa McPherson Trust (LMT) an organization which brought a civil suit against The Church of Scientology for the wrongful death of Lisa McPherson and provided help and consolation for ex-Scientologists who had negative experiences of the cult. The trust operated out of Clearwater, Florida (Scientology's "spiritual" headquarters); frequent confrontations between the LMT and Scientology would ensue. 
Minton’s turn came after a Scientology probe onto his financial affairs. Minton was repeatedly ordered to attend depositions and grilled by Scientology lawyers about his alleged financial dealings. In addition, years later former church members detailed how Scientology investigated Minton finding information he was "worried about". Critics of Scientology believe that Minton was blackmailed by the Church of Scientology. On March 16 2002 Minton called Mike Rinder and on April 6 of that year they met. At that meeting Minton told Rinder that there were lies told in the case, he feared Scientology would uncover those lies in court and he would be sent to jail for perjury.
|“||I don't want my life defined by Scientology anymore. I just want some peace.||”|
—Bob Minton, 
During a April 20, 2002 hearing in the Lisa McPherson wrongful death lawsuit against the Church of Scientology, Minton spoke against Ken Dandar, the attorney representing McPherson's family. In a 26-page affidavit, Minton stated that Tampa attorney Ken Dandar asked him to lie, drew up false court records for him to sign and urged him to generate bad publicity for the Church of Scientology to prejudice potential jurors in the McPherson wrongful death case as Scientology tries to get the wrongful death case dismissed on grounds of serious misconduct by Ken Dandar and his client.[15 ] Minton's affidavit gave new details about how involved Minton was in the wrongful death case from the start, stating that he gave Dandar more than $2 million to finance the case and paying witnesses to testify against the church.[15 ] Dandar took the witness stand to explain the origin of Swiss bank checks totaling $750,000 that Minton allegedly gave him.[15 ] Minton also testified about two financial arrangements in which $800,000 of his money was transferred from Europe to the Lisa McPherson Trust and that he had kept a portion of that money because he wanted to hide the source of the Trusts funding from the Church of Scientology.[16 ]
Despite the allegations the presiding judge declined to remove attorney Dandar from the case, stating that she did not believe Minton's testimony, and that he had lied in an attempt to escape income taxes. Six months before she had already remarked that it was irrelevant how much money Minton had put into the case. 
In August 2009, John Fashanu, who in 2000 accused Minton and Ibrahim Babangida of stealing money from Nigeria, apologized saying "I can say it again and again, that there was nothing like debt buy-back or any billions stacked away in any account anywhere." In 2000, Minton said that Fashanu was given false information by the Church of Scientology to attack him.
In October 2009, Rinder and Marty Rathbun revealed to the St. Petersburg Times how Scientology silenced Minton by digging into his financial details and secretly recording conversations. This included the Nigeria allegations in 2000. Rinder told the Times: "There were things that, really, he was worried about and had caused problems for him in the investigation that we had done" and Minton and church reached a private settlement. Rinder, who left the church in 2007, now considers Minton a friend.