The latter is designated as an anti-LGBTQ hate group by the Southern Poverty Law Center, and also publishes Klingenschmitt's TV show, Pray in Jesus Name.

Klingenschmitt left the Air Force as a major[11] on 2 September 2002, accepting a demotion (to lieutenant) to become a military chaplain in the United States Navy.

[12][10] Klingenschmitt was quickly disillusioned at Chaplaincy School, finding that the military's religious pluralism for servicemembers of all faiths ran contrary to his evangelism, despite the National Conference on Ministry to the Armed Forces' code of ethics stating that chaplains must "function in a pluralistic environment".

[16] In March 2005, Carr recommended that Navy Personnel Command not extend Klingenschmitt's active-duty tour,[13] saying the lieutenant "demonstrated recurring confusion concerning a chaplain's role within a military organization.

[18] Later that year, in protest of the Navy's position on his religious proselytization, Klingenschmitt collaborated with US Representative Walter B. Jones Jr. to pressure President George W. Bush to issue a military–religious executive order that would guarantee "the right of chaplains to pray 'in the name of Jesus.

'"[10] While on official leave in late December 2005,[19] in an effort to prevent his anticipated dismissal from the Navy, and hoping to force President Bush's hand, Klingenschmitt began an 18-day hunger strike in front of the White House to protest the Navy "mandating nonspecific language in public, nondenominational events, and an order from superior officers prohibiting him from wearing his uniform during television appearances related to his protest".

The Navy responded to Klingenschmitt's event by releasing a memorandum affirming their position "that sailors cannot wear their uniforms for media appearances without prior approval from command, but are permitted to do so for any legitimate worship services".

[15] Despite having declared he would only consume water "until the president of the United States gives me back my uniform and lets me pray publicly in Jesus' name",[20] Klingenschmitt pointed to this Navy memo as his victory on 7 January 2006.

He told the assembled press that "Today the Navy has reluctantly obeyed the law, to grant me the religious liberty I always should've had"; the military elaborated that there had been no changes in policy, and had not given Klingenschmitt carte blanche permission to publicly wear his uniform.

[22] After verifying that Pyle's orders restricted uniform-wear to "attending or participating in a bona fide religious service or observance", Klingenschmitt led prayers in uniform for a clergy lobbyist group's demonstration in Lafayette Square, Washington, D.C. before immediately removing parts of his uniform, replacing them with a clerical collar, and making statements to the assembled press.

[10] Captain Pyle issued a letter of caution to Klingenschmitt for violating Article 89 of the Uniform Code of Military Justice (UCMJ) by disrespecting senior commissioned officers via "intemperate language" on the chaplain's personal website.

Ordered to remove the offending material, Klingenschmitt did so, but cited the Military Whistleblower Protection Act in warning that "[w]hile I consented this one time to modify the content of my communications to Congress, I shall not do so again.

[19] Klingenschmitt prayed at the event, and distributed a document detailing both his complaints about Navy policy, as well as his explicit intent to disobey orders about appearing in uniform.

[19] He was formally charged with one count of Article 92 of the UCMJ (failure to obey order or regulation) on 3 August, whereafter he pled not-guilty and requested trial by jury.

[19] Klingenschmitt's first motion to dismiss claimed that Pyle's order was not lawful under the First Amendment to the United States Constitution, and his second alleged that CNRMA had a personal investment in the trial's outcome and could not convene the court-martial; both were denied.

Represented by a military public defender[11] and private civilian attorney on 13 September,[10] Klingenschmitt testified that his 30 March actions were permissible because the news conference was "a bona fide worship service or observance".

Processing for separation in accordance with Section 643 of [Title 10 of the United States Code] shall be initiated immediately upon such notification.Under regulations prescribed by the Secretary of Defense, a commissioned officer on the active-duty list of the Army, Navy, or Air Force who is appointed or designated as a chaplain may, if he fails to maintain the qualifications needed to perform his professional function, be discharged or, if eligible for retirement, may be retired.

[10] An advisory board, the Chief of Naval Personnel, the Chief of Chaplains, and the Assistant Secretary of the Navy for Manpower and Reserve Affairs concurred against approving Klingenschmitt's new endorsement, based on professional unsuitability, disciplinary record, and unsatisfactory performance: "The Secretary concluded that you do not possess the character, leadership, or professional traits needed to successfully serve as a naval officer.

Captain Holcomb wrote at length to the Kentucky House to not only refute Klingenschmitt's specific claims about the court-martial, but to characterize his ex-chaplain as "totally untruthful, unethical and insubordinate".

[31] Klingenschmitt publicly prayed for death and other curses to befall Barry W. Lynn (of the Americans United for Separation of Church and State) and Michael L. Weinstein (of the Military Religious Freedom Foundation).

His targets were beset with "death threats, had a swastika emblazoned on their home in New Mexico, animal carcasses left on their doorstep and feces thrown at the house."

[26] On 2 April 2012, Judge Martin Hoffman dismissed the lawsuit for lack of evidence connecting Klingenschmitt's exhortations with the threats and damages inflicted.

[34] When he used the platform to call a transgender six-year-old a demon, the organization was added to the Southern Poverty Law Center's anti-LGBTQ hate list.

[43] That August, Klingenschmitt was again disavowed by his own party, as well as condemned by Colorado House Speaker Mark Ferrandino, for claiming that then-Representative Jared Polis wanted to behead Christians in the United States like ISIS did in Syria;[44] he later walked back those remarks.

[51] When he was criticized by the public, the Colorado Republican party, and former House minority leader Mark Waller,[37] Klingenschmitt initially refused to retract the comments, repeating them on Pray in Jesus Name.

[51] With few disciplinary measures available, current minority leader Brian DelGrosso removed Klingenschmitt from his position in the Health, Insurance and Environment Committee on 30 March.

[54] After the Boy Scouts of America ended their prohibition of homosexual leaders in July 2015, Klingenschmitt criticized the organization for putting children in danger of molestation.

[62] In 2019, Klingenschmitt ran for one of three at-large seats on the Colorado Springs city council, on a platform opposing taxation and predominant left-wing politics.

[66] His belief in Christianity similarly drove opposition those same people being allowed to serve in the United States Armed Forces: during political discussions about repealing don't ask, don't tell, he advocated against the 112th United States Congress certifying the military as ready for such a change, and to "instead pass strong law's [sic] protecting the rights of Christian troops".