Her second album, I'm With Stupid (1995), was also released by Geffen records, after they signed her based on the success of her debut album. It too, received positive reviews, but only managed modest commercial success.
In 1999, she started recording material for a new album, but because her record label rejected it, they instructed her to go away and re-record more radio-friendly pop hits. She negotiated a contract release from Geffen Records – in which they sold her album back to her – and later founded her own label, SuperEgo Records.
Mann became one of the first independent artists to end her contract with her label, without paying them a dime. The dissolution of her contract was in part a mutual blessing, as Geffen Records felt she was difficult to work with, and she wanted to leave and go independent.
In 2000, Mann released the album that she had previously worked on for Geffen Records, Bachelor No. 2 or, the Last Remains of the Dodo, on her own label through her website for her fans, and sold copies at live gigs. The album went on to be a worldwide success.
Her fifth studio album, The Forgotten Arm (2005), was a concept album set in the 1970s, about two lovers who meet at the Virginia State Fair and go on the run.
A year later Mann entered into the trend of artists who recorded Christmas albums, One More Drifter in the Snow (2006). The only difference with her album however is that even though it was mostly full of covers, she wrote fresh material for the album.
@#%&*! Smilers, was released in 2008. Mann stated that the title of the album comes from a thread she read 27 years ago on a newsgroup, where someone was complaining about the "******* smilers" who would approach him at work when he was in a bad mood and try to cheer him up.
In 2012, Mann released her eighth solo studio album, Charmer, which was received with mixed reviews from both critics and fans.
As of 2013, Mann began collaborating with indie/punk multi-instrumentalist Ted Leo, performing as Indie Rock duo, The Both. They released their eponymous debut in 2014.