In New York City, in 1996 she released her first album, Imaginaryland, consisting mostly of original a cappella music. In 2000, Petra was struck by a car while crossing a street in Los Angeles; the resulting injuries forced her out of performance for several months. In 2005 she released the home-recorded album Petra Haden Sings: The Who Sell Out (Bar/None), a complete a cappella rendition of The Who Sell Out. The project was suggested to Haden by longtime friend Mike Watt, who also gave her the eight-channel multi-track cassette recorder she used to make it. Funded in part by a Durfee grant and wanting to perform the work live, Haden created a new arrangement of The Who Sell Out for a ten woman a cappella choir called Petra Haden & The Sellouts. The premier live performance of the full work occurred in July 2005 at the Ford Amphitheatre as a part of the "sound." concert series.
She has also released a self-titled collaboration with jazz guitarist Bill Frisell.