The song is in the key of A major, although MacDonald gives B minor as a secondary key. The opening organ part ends with a preview of the melody over which the song title appears in the song proper. After this short introduction, the composition is structured into two portions, each consisting of two verses and a chorus, which are followed by a single verse, a final chorus and an outro, with some of these sections rendered as instrumental passages. The composition is a meta-song, in that its subject is the work itself. While commenting on the pointlessness of writing for Northern Songs, Harrison employs musical dissonance to express his dissatisfaction with the company. In musicologist Walter Everett's description, this is achieved through the use of "ill-behaved tones" and "wrong-mode" chords. From the verse's opening A major chord, the melody moves to a ii minor voicing, rendered as B minor 7/11 through the inclusion of a low-register E note. In his lyrics, Harrison acknowledges the apparent awkwardness of such a change, singing "You may think the chords are going wrong" and, in the final verse, that the harmony "might be a little dark and out of key". Musicologist Alan Pollack considers the song's music and lyrical message to be "uncannily in tune" with one another, and that this effect is accentuated by surprising and irregular phrase-lengths in the verses. In contrast to the minimal chord changes over the verses, the choruses present a fast progression of chords – specifically, E major, B minor 7, G major, C7 and F7. In the first chorus, Harrison comments that, given the inadequacy of his publishing arrangement, "It doesn't really matter what chords I play". Author Ian Inglis interprets this line as mirroring the singer's complaint to Beatles biographer Hunter Davies in the late 1960s, regarding the futility of the band's live performances when their screaming fans never listened to the music the Beatles were playing. Harrison biographer Simon Leng describes "Only a Northern Song" as the first example of its composer "pushing back at the Beatles as an organization he found wanting", a theme Harrison returned to in 1968 with "Not Guilty", with his comments on the group's internal discord. The Beatles taped the basic track for "Only a Northern Song" at EMI Studios (now Abbey Road Studios) on 13 February 1967, during the sessions for "Sgt. Pepper's Lonely Hearts Club Band".