Produced by David Anderle with numerous well-known musicians including Stephen Stills, the album had a rock-country-arthouse feel, typically eclectic for Collins, and included her own composition "My Father", as well as Ian Tyson's "Someday Soon" (which would go on to become one of Collins' signature songs), two Leonard Cohen compositions – "Story of Isaac" and "Bird on the Wire" – and the traditional murder ballad "Pretty Polly"; and the title song, "Who Knows Where the Time Goes?", composed by Sandy Denny.

Two versions of the song "Who Knows Where the Time Goes?" were released. Version 1 with only vocal, two guitars, and bass appeared on the B side of "Both Sides Now", on the soundtrack to the 1968 film The Subject Was Roses, and on the compilation album Colors of the Day. Version 2 is a composite. The first verse is the same take as version 1, but with everything remixed to the left channel, and it then crossfades to a different recording with a larger arrangement and modulates to different key. Version 2 appears on the album Who Knows Where the Time Goes?.

Collins' cover of Joni Mitchell's "Chelsea Morning" was recorded during the Who Knows Where the Time Goes sessions, but was ultimately not included on the album; however a single release of the song, with "Pretty Polly" as the B-Side, charted during early 1969.

"Hello, Hooray", written by Canadian singer/songwriter Rolf Kempf, was later covered as the opening track on Alice Cooper's 1973 album Billion Dollar Babies.

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