In 1994 Chocolate and Cheese was released, which spawned the singles "Voodoo Lady", "Freedom of '76", and "I Can't Put My Finger on It".

It is considered a prog rock concept album, and featured the singles "Mutilated Lips" and "Ocean Man", the latter gaining a significant following after being a song on the SpongeBob SquarePants Movie soundtrack.

The band's desire to pursue alternate forms of media led to the MP3-only release Craters of the Sac, presented by Melchiondo for online download and free trade.

However, according to Melchiondo, once the album was completed, Elektra realized the sales potential of the CD and denied Ween the right to release it through their independent label.

The pop-themed, Lennon-McCartney-inspired album produced two singles: "Even If You Don't", which was made into a music video directed by Trey Parker and Matt Stone, and "Stay Forever".

In 2011, Melchiondo quietly released an MP3-only collection of songs called The Caesar Demos, named after the band's original working title for Quebec, to friends on his Facebook page.

In his comment, he stated the songs were all recorded between 2001 and 2003 while Claude Coleman was recovering from injuries sustained in a car accident, and that many of the tracks featured only himself and Freeman.

The band broke up in 2012, after Freeman commented in a Rolling Stone interview that it was time to pursue solo projects.