Manic Street Preachers guitarist Richey Edwards wrote the lyrics, marking one of his last contributions to the band. Edwards disappeared in February 1995 and was never found. The band soldiered on without him, not knowing if he was dead or in hiding. Everything Must Go was the first album released in his absence, and it contained five songs he co-wrote.
"Small Black Flowers That Grow In The Sky" empathizes with a zoo animal's state of mind while in captivity, an insight into how Edwards was feeling. Manic's bass player Nicky Wire, who was very close to Edwards, told Dazed & Confused that Edwards wrote the song about "getting born in zoos and just going mad with boredom." Wire added, "But if you read it, you'd just think it was about him."
This gentle number is a rare rock song with a harp; it was played by Julie Aliss, who also appeared on the 1987 Siouxsie and the Banshees album Through the Looking Glass.