Professors John Covach and Graeme M. Boone have written: "An exquisite exercise of harmonic virtuousity, 'Our Prayer' allowed the Beach Boys once again to show off their vocal abilities and stylistic influences earlier demonstrated on such songs as 'Their Hearts Were Full of Spring'."
I was sitting at my piano thinkin' about holy music. I poked around for some simple but moving chords. Later I sat down and wrote 'Our Prayer' in sections. The boys were overtaken by the arrangement. I taught it to them in sections, the way I usually do. The purity of the blending of the voices made the listeners feel spiritual. I was definitely into rock church music.
The wordless, a cappella piece was originally supposed to be the opening track to the Smile album. As Beach Boys historian Peter Reum explained, "Brian intended for 'Our Prayer' to be the opening track, a spiritual invocation, for 'Smile'. It was the first track to be recorded for the album but was initially considered an opening for 'Heroes and Villains'." The title may be a reference to the 1939 traditional pop standard "My Prayer", written by Georges Boulanger and Jimmy Kennedy. As music journal Paul Williams elaborates,
It's a wonderful wordless beginning for a record that for the most part uses words the same way it uses strings and keyboards—for their sounds. This is in sharp contrast to Pet Sounds where most of the songs have titles and lyrics that evoke specific situations and feelings. Smile's radicalism begins with and centers around the fact that it is abstract, whereas all previous Beach Boys records and most rock-and-roll songs are concrete in their imagery. They have words, and those words generally tell a story.
Wilson was to quickly record and get it over with as soon as possible so he could focus on recording the bulk of Smile for the January, 1967 release that he had promised Capitol Records. However, Smile was abandoned, and the track lay dormant for several months. The song was eventually released together with "Cabinessence" on their 1969 album 20/20, albeit with some added vocal overdubs. The main vocals were recorded in late 1966 with the additional vocals being recorded at Capitol Records Studios two years later.