In late 1966, "Sunday Morning" was the final song to be recorded for The Velvet Underground & Nico. It was requested by Tom Wilson, who thought the album needed another song with lead vocals by Nico with the potential to be a successful single. The final master tape of side one of the album shows "Sunday Morning" only penciled in before "I'm Waiting for the Man".
Wilson brought the band into a New York City recording studio in November. The song was written with Nico's voice in mind by Lou Reed and John Cale on a Sunday morning. The band previously performed it live with Nico singing lead, but when it came time to record it, Lou Reed sang the lead vocal. Nico would instead sing backing vocals on the song.
Aiming to create a hit for the album, "Sunday Morning" features noticeably more lush and professional production than the rest of the songs on the album. The song's prominent use of celesta was the idea of John Cale, who noticed the instrument in the studio and decided to use it for the song.
A cover of the song by the Doug Anthony All Stars was used in a season 1 episode of DAAS Kapital, but did not appear on the DVD set of the sci-fi sitcom due to "contractual reasons... and because we never paid to use it in the first place," according to Paul McDermott.