On March 19, 1987, after the disclosure of a payoff to Hahn, Bakker resigned from PTL. Although he acknowledged that he had a sexual encounter with Hahn at a hotel room in Clearwater, Florida, he denied raping her. Bakker was also the subject of homosexual and bisexual allegations made by Fletcher and PTL director Jay Babcock, which Bakker denied under oath. Rival televangelist John Ankerberg appeared on Larry King Live and made several allegations of moral impropriety against Bakker, which both Bakkers denied.
Bakker believed that Falwell would temporarily lead the ministry until the scandal died down, but on April 28, 1987, Falwell barred Bakker from returning to PTL upon hearing of allegations of illicit behavior which went beyond the Hahn allegations. Later that summer, as donations declined sharply in the wake of Bakker's resignation and the end of The PTL Club, Falwell raised $20 million to keep Heritage USA solvent and took a promised water slide ride at the park. Falwell and the remaining members of the PTL board resigned in October 1987, stating that a ruling from a bankruptcy court judge made rebuilding the ministry impossible.
A sentence-reduction hearing was held on November 16, 1992, and Bakker's sentence was reduced to eight years. In August 1993, he was transferred to a minimum-security federal prison in Jesup, Georgia. Bakker was paroled in July 1994, after serving almost five years of his sentence. His son, Jay, spearheaded a letter-writing campaign to the parole board advocating leniency. Celebrity lawyer Alan Dershowitz acted as Bakker's parole attorney, having said that he "would guarantee that Mr. Bakker would never again engage in the blend of religion and commerce that led to his conviction." Bakker was released from Federal Bureau of Prisons custody on December 1, 1994, owing $6 million to the IRS.
Bakker's revived show features a number of ministers who bill themselves as "prophets". He now says that "PTL" stands for "Prophets Talking Loud".
In an October 2017 video, Bakker said that "God will punish those" who ridicule him; he has said that Hurricane Harvey was a judgment of God, and he blamed Hurricane Matthew on then-President Barack Obama. Bakker predicted that if then-President Donald Trump was impeached, Christians would begin a Second American Civil War. He compared the 2017 Washington train derailment to the sinking of the RMS Titanic and stated the Amtrak train derailment was a warning from God. He also claimed that he predicted the September 11 attacks of 2001, stating that he "saw 9/11 in 1999 before New Year's Eve" and that there would "be terrorism" and bombings in New York City and Washington, D.C." A few days after the Stoneman Douglas High School shooting, he stated that "God came to [him] in a dream... and he was wearing camouflage, a hunting vest and had an AR-15 strapped to his back" and that God supported Trump's plan to arm teachers. Following the death of Billy Graham on February 21, 2018, Bakker attended Graham's funeral and paid his respects, stating that Graham was the greatest preacher since Jesus, and also remarking that Graham had visited him in prison.
In April 2020, prohibited from receiving credit card transactions, Bakker disclosed to his viewers that his ministry was on the brink of filing for bankruptcy and urgently petitioned them for donations.
The following month, GEB America and World Harvest Television dropped Bakker's program from their networks after DirecTV owner AT&T asked channels to reconsider airing the show. AT&T made the request of its channels in response to a deplatforming campaign from the liberal Christian group Faithful America.
On May 8, 2020, Lori Bakker announced that Jim Bakker had suffered a stroke that his son Jay described as "minor". Lori stated that he would be taking a sabbatical from the program until he recovers. She blamed the stroke on Bakker's hard work on his show and wrote that he had described the criticism against him as "the most vicious attack that he has ever experienced". Bakker returned to his program for the first time following his stroke on July 8, 2020.
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Mantlya, Kyle (January 3, 2018). "Jim Bakker: Washington Train Derailment Was A Warning From God". Right Wing Watch. Archived from the original on February 26, 2018. Retrieved February 25, 2018. Jim Bakker: The great preachers of all times have said the Titanic is God's warning http://www.rightwingwatch.org/post/jim-bakker-washington-train-derailment-was-a-warning-from-god/
"Televangelist Jim Bakker claims he predicted 9/11 disaster". Jolt Left. August 23, 2011. Archived from the original on February 26, 2018. Retrieved February 25, 2018. Jim Bakker: I saw 9/11 in 1999 before New Year's Eve ... I said there's going to be terrorism; there's going to be a bombing in New York and Washington DC. I said it would be at a high defense location in DC ... https://joltleft.com/televangelist-jim-bakker-claims-he-predicted-911-disaster/
"Jim Bakker Supports Arming Some Teachers: 'Jesus Loves AR-15'". nova-magazine.net. February 22, 2018. Archived from the original on March 6, 2018. Retrieved March 5, 2018. To me, that is a sign that he is against gun control. God ordained Donald Trump and he supports his plan to arm teachers. https://web.archive.org/web/20180306142257/https://www.nova-magazine.net/jim-bakker-supports-arming-some-teachers-jesus-loves-ar-15/
Marusak, Joe; Funk, Tim (February 27, 2018). "Fallen evangelist Jim Bakker and wife pay their respects to Billy Graham in Charlotte". The Charlotte Observer. Archived from the original on February 28, 2018. Retrieved March 5, 2018. http://www.charlotteobserver.com/news/special-reports/billy-graham-life/article202470224.html
Dyches, Chris (February 27, 2018). "Fallen PTL pastor Jim Bakker recalls prison visit from Rev. Billy Graham". Charlotte, N.C.: WBTV. Archived from the original on March 6, 2018. Retrieved March 5, 2018. http://m.wbtv.com/story/37607004/fallen-ptl-pastor-jim-bakker-recalls-prison-visit-from-rev-billy-graham
Gryboski, Michael (August 31, 2017). "Pastors Network Pres: Jim Bakker Is Wrong, Christians Won't Start 'Civil War' Over Trump Impeachment". The Christian Post. Archived from the original on February 14, 2018. Retrieved February 13, 2018. https://www.christianpost.com/news/pastors-network-president-jim-bakker-wrong-christians-wont-start-civil-war-over-trump-impeachment-197355/
Saunders, Martin (May 1, 2018). "Jim Bakker's TV show amounts to spiritual abuse – so why is he still broadcasting?". Christian Today. Archived from the original on May 2, 2018. Retrieved May 1, 2018. https://www.christiantoday.com/uk/jim-bakkers-tv-show-amounts-to-spiritual-abuse-so-why-is-he-still-broadcasting/128881.htm
"NY AG Letitia James orders televangelist Jim Bakker to quit advertising coronavirus cure". New York Post. March 6, 2020. Archived from the original on March 6, 2020. Retrieved March 6, 2020. https://nypost.com/2020/03/06/ny-ag-letitia-james-orders-televangelist-jim-bakker-to-quit-advertising-coronavirus-cures/
"FDA, FTC sends warning letter to Jim Bakker Show". Ozarks Independent. March 9, 2020. Archived from the original on April 6, 2020. Retrieved March 9, 2020. https://web.archive.org/web/20200406135333/http://ozarksindependent.com/2020/03/09/fda-ftc-sends-warning-letter-to-jim-bakker-show/
"Federal government, Missouri AG tell area pastor to stop claiming coronavirus cure". Branson tri-lakes News. Archived from the original on March 11, 2020. Retrieved March 11, 2020. http://bransontrilakesnews.com/news_free/article_d2e39562-62fd-11ea-a417-1b9ee625bd44.html
"Jim Bakker sued by second state for selling fake coronavirus cure". CBS News. June 17, 2020. Archived from the original on July 17, 2020. Retrieved July 16, 2020. https://www.cbsnews.com/news/jim-bakker-sued-by-second-state-for-selling-fake-coronavirus-cure/
Salter, John (May 5, 2020). "Jim Bakker seeks dismissal of suit claiming he touted false virus cure". Star Tribune. Archived from the original on May 7, 2020. Retrieved May 6, 2020. https://www.startribune.com/jim-bakker-seeks-suit-dismissal-ex-governor-is-his-lawyer/570207402/
Slisco, Aila (April 22, 2020). "Televangelist asks viewers to send checks after credit card companies cut him off for selling fake coronavirus cure". Newsweek. Archived from the original on April 26, 2020. Retrieved April 23, 2020. https://www.newsweek.com/televangelist-asks-viewers-send-checks-after-credit-card-companies-cut-him-off-selling-fake-1499636
Holman, Gregory J. (May 6, 2020). "Liberal Christian group says TV network tied to Oral Roberts University drops Bakker show". USA Today. Retrieved May 8, 2020. https://www.usatoday.com/story/news/local/missouri/2020/05/06/jim-bakker-show-oral-roberts-university-geb-network-faithful-america/5175969002/
Marusak, Joe (May 8, 2020). "TV pastor Jim Bakker suffers stroke, wife and son confirm. 'Jim will be back!'". The Charlotte Observer. Archived from the original on May 10, 2020. Retrieved May 8, 2020. https://www.charlotteobserver.com/news/local/article242596441.html
Marusak, Joe (May 8, 2020). "TV pastor Jim Bakker suffers stroke, wife and son confirm. 'Jim will be back!'". The Charlotte Observer. Archived from the original on May 10, 2020. Retrieved May 8, 2020. https://www.charlotteobserver.com/news/local/article242596441.html
Marusak, Joe (July 8, 2020). "TV pastor Jim Bakker returns to his show for the first time since suffering a stroke". The Charlotte Observer. Archived from the original on July 10, 2020. Retrieved July 16, 2020. https://www.charlotteobserver.com/entertainment/tv/article244094697.html
Wert, Jason (June 23, 2021). "Attorney General settles suit with Jim Bakker". KWTO (AM). Archived from the original on June 23, 2021. Retrieved June 23, 2021. https://933kwto.com/attorney-general-schmitt-settles-suit-with-jim-bakker/