The scene in which Scorpius coldly shoots the alternate version of Rygel was a deliberate reminder to the audience that Scorpius had not lost any of his edge since coming on board Moya.
Producer Andrew Prowse notes that "Prayer" is "probably the closest translation from script to screen of any Farscape episode."
David Kemper was concerned about the scene showing the "abortion" of the fetus, until it was pointed out that this was later clearly shown to be a fake.
The producers fully expected that the shots of the fetus being aborted would be cut for its UK transmission by the BBC. And they were right.
Because of the unusual nature of "A Constellation of Doubt," the scenes on Moya for that episode were filmed after "Prayer" was completed.
According to Claudia Black, the original plans for the flashback sequences involving Aeryn's lovers would have seen them "humping against a wall." She felt that wasn't appropriate, and that kissing would be better.
Claudia Black describes the chair that she had to sit in as like something from the film Dead Ringers. Foot holes had to be drilled into the chairs at the last minute to help the actors recover between scenes.
Designer Tim Ferrier enjoyed creating the torture chairs, although he wasn't sure whether the producers would like them. He didn't need to worry; they loved hem.
David Kemper was so impressed by Jason Clarke's performance as Jenek in this episode that he wrote him into the final episodes of the season.
Sandy Gore returned to Farscape to play Vreena, after originally appearing as on of the Litigaran Judges in the original opening episode of Season 2, "Dream A Little Dream."