Thom Yorke has removed his solo album The Eraser from Spotify, along with Amok, the album recorded with producer Nigel Godrich and Flea from the Red Hot Chili Peppers under the band name Atoms for Peace.
The singer tweeted that Godrich and he had done so to stand up "for our fellow musicians". They claim that Spotify's payment model is damaging new and emerging artists. "Make no mistake new artists you discover on #Spotify will not get paid," Yorke tweeted. "Meanwhile shareholders will shortly being rolling in it. Simples."
The albums have also been removed from rival service Rdio.
"I think the point is that streaming suits catalogue, but cannot work as a way of supporting new artists' work," added long-term Radiohead collaborator Godrich on his Twitter feed. "Spotify and the like either have to address that fact and change the model for new releases or else all new music producers should be bold and vote with their feet."
Radiohead's albums are so far unaffected by the boycott, and are still available on both Spotify and Rdio.
Spotify says it has paid £332 million ($500 million) to rights holders since its launch in Sweden in 2008, and the user base has grown so much - to over 24 million active users, six million monthly subscribers - that it expects to pay a further £332 million this year alone.
Fans of Yorke have also taken to Twitter to complain about the decision, including some directed at the singer himself. "Your small meaningless rebellion is only hurting your fans," wrote one. "A drop in the bucket really."