"Amen" has received much backlash from religious organizations. On July 11, 2012, Meek Mill called into Philadelphia radio station Hot 107.9 and argued with Philadelphia pastor and rapper Jomo K. Johnson about the song. Johnson pushed for a boycott of the song, and will soon publish a book about Mill and MMG accusing them of blasphemy. Mill has subsequently apologized to those who might have been offended by the song, and Johnson has withdrawn his calls for a boycott.
The controversy garnered reactions from several gospel hip hop artists. In an interview with Billboard, Lecrae was asked what he thought of the controversy, and he responded:
It's going to sound funny, but it doesn't bother me if a person doesn't understand the root or the base meaning of something, or if they don't value that thing to speak about it. It's almost like being mad at a blind person for bumping into you. You don't get mad at the blind person for bumping into you, you show them where the seat is, so I'm more interesting [sic] in helping people understand what those terms mean verses [sic] getting mad at its misuse.
The Ambassador and Da T.R.U.T.H. also commented on the controversy in interviews by saying that they greatly appreciated that Johnson took a public stand against the song, though Da T.R.U.T.H. stated that there is a possibility that Johnson could have reasoned more with Meek Mill in the radio debate instead of just making blanket statements.
On August 2, 2012, Game released a remix of the song. On September 3, 2012, Lil Wayne released a remix of the song on his mixtape Dedication 4. Slim Thug also released a remix of the song on his mixtape entitled Thug Thursday.