Cloud Cult developed in 1995 as a solo studio project of Craig Minowa. His first full-length album, The Shade Project caught the interest of a few small independent labels who urged Minowa to consider performing the songs live. Craig worked the next four years on a new studio project which would be the first official Cloud Cult album, Who Killed Puck?.

In 1999, Craig and Connie Minowa formed Earthology, a not-for-profit environmental organization that would later gain its nonprofit 501c3 status. Craig worked on developing the Earthology Records branch, which was focused on helping to green the music industry. Earthology Records would become the homegrown powerhouse where all of the band's booking, publicity, CD replication, t-shirt production, and recording would take place. Through Earthology, Minowa developed the first 100% postconsumer recycled CD packaging in the U.S. market.

Earthology Records was later moved to an organic farm, powered by geothermal energy and built partially from reclaimed wood and recycled plastic. The band began zero net greenhouse gas practices for tours long before it was trendy to be green. The band's merchandise is 100% postconsumer recycled or made of certified organic materials. Cloud Cult has planted several thousand trees to absorb the band's CO2 output. They also donate heavily to projects that build wind turbines as revenue generators on Native American Reservations.

In the year 2002, shortly after the unexpected death of his two-year-old son Kaidin, Minowa wrote over a hundred songs to deal with the loss. They Live on the Sun was finished in 2003 and went to #1 on college radio station charts across the country. Since that album, Cloud Cult's music has been strongly inspired by the "big picture" issues of life: "who are we, why are we here, where did we come from, where do we go". Minowa seems in constant pursuit of the light at the end of the tunnel.

In 2004, released Aurora Borealis just six months after They Live on the Sun. Shortly after, Cloud Cult was nominated by the Minnesota Music Awards as “Artist of the Year” along with Prince and Paul Westerberg. With a van covered in solar panels, the band began touring nationally. Cloud Cult's stage show began to garner the attention of national press, as they included two live painters on stage, Connie Minowa and Scott West, as well as back screen video and performance artists. In 2006, Cloud Cult released Advice from the Happy Hippopotamus, which Pitchfork Media called “insane genius” and rated the album with an 8.3.

The Denver Post ranked the 2007 release The Meaning of 8 as one of the top ten albums of the past decade, along with bands like Modest Mouse, The Flaming Lips and Radiohead. Cloud Cult received several offers from major record labels, but all were rejected in favor of self-publishing and maintaining total control over the ethical aspects of the business practices. Cloud Cult released the album entitled Feel Good Ghosts (Tea-Partying Through Tornadoes) on April 8, 2008. As with the past Cloud Cult albums, the album was recorded and produced at Minowa’s small organic farm in Northern Minnesota. "The place is so far out in the boonies, you can barely find it, because it’s not on the maps," said Dan Montalto, an MTV Producer who brought a camera crew to the farm to film a short MTV feature on the band.

In October 2008, Cloud Cult was featured in an animated Esurance commercial that aired during the Super Bowl. The band is shown playing their song "Lucky Today" while floating on clouds and promoting ecological driving practices. In exchange for the work, Esurance helped fund some of the band's costs for greening the recording of albums. During 2008 and 2009, the band's growth continued, with a heavy tour schedule and appearances on MTV, Carson Daly, Rolling Stone, Spin and a plethora of other media outlets.

In the Spring of 2009 Cloud Cult released No One Said It Would Be Easy, a full-length documentary about the band created by John Burgess and Scott West, as well as Lost Songs from the Lost Years", a collection of previously unreleased songs spanning the band's 15 year history. The band took up touring again with the 2010 release of Light Chasers, which was an elaborate concept album about the lifelong spiritual quest. Meanwhile, Craig increased his workload of scoring Cloud Cult type music for National Geographic and other documentaries. The band released a new full-length album on March 5, 2013, entitled Love which charted higher on the Billboard Charts for Cloud Cult than any of their previous albums.

Cloud Cult released a new full length live acoustic album and concert film, Unplug, on April 15, 2014. It was produced and mixed by Jeff D. Johnson who has been doing Cloud Cult’s live sound for the past seven years. The album was then mastered by Jeff Lipton (Bon Iver, Arcade Fire). While the songs were all pulled from the band’s existing discography, the versions on Unplug are quite different than the album versions.

Cloud Cult made their European debut in the summer of 2014 and released their newest album, The Seeker, in February of 2016 with the current lineup of Shannon Frid-Rubin (violin), Shawn Neary (bass/trombone), Sarah Perbix (keys/horns), Daniel Zamzow (cello/mandola), Jeremy Harvey (drums), as well as Scott West and Craig and Connie Minowa. The album has been lauded by critics as the band's best work to date. The album was also made into a feature length film, starring Josh Radnor and Alex McKenna, written by Minowa and directed by Jeff D. Johnson. The film was released in late 2016.