[6] Ashley Capps, co-founder of AC Entertainment, developed Bonnaroo following the cancellation of the Hot Summer Nights rock music festival in Knoxville, Tennessee in 1999.

Hot Summer Nights, which was a mainstay in Knoxville's World's Fair Park would suspend operations permanently following construction by city officials.

Capps would state that the cancellation would be the main drive behind the origin of Bonnaroo, "The closing of the World's Fair Park for concerts precipitated getting creative and trying to find, 'OK, if we can't do this anymore, how can we still participate in the summer outdoor concert business,' and it was from that that Bonnaroo was ultimately launched.

In 2019, after a record breaking festival sell out, it was announced that Live Nation was buying out Superfly's share of Bonnaroo.

[12] The 2020 event was initially pushed back three months until September 2020, and then ultimately cancelled because of health concerns surrounding the COVID-19 pandemic in the United States.

[34] R&B singer D'Angelo marked his return to American stages for the first time in over 12 years[35] on June 9, 2012, with a surprise performance at the festival's annual Superjam.

He was backed by members of the R&B collective the Soulquarians, most notably Questlove, James Poyser and Pino Palladino, with guest guitarist Jesse Johnson.

[37] Other performers have included Widespread Panic (2002, 2003, 2005, 2007, 2008, 2011), Phish (2009, 2012, 2019), The Dead (2003, 2004), Dead & Company (2016), U2 (2017), Pearl Jam (2008, 2016), Billy Joel (2015), Mumford & Sons (2011, 2015), Elton John (2014), Eminem (2011, 2018), Jack White (2010, 2014), Lionel Richie (2014), the Flaming Lips (2003, 2007, 2010, 2014), Paul McCartney (2013), Tom Petty and the Heartbreakers (2006, 2013), Wu-Tang Clan (2013), Red Hot Chili Peppers (2012, 2017, 2024), Radiohead (2006, 2012), Neil Young (2003, 2011), Dave Matthews Band (2005, 2010), Stevie Wonder (2010), Bruce Springsteen and the E Street Band (2009), Nine Inch Nails (2009), Metallica (2008), the Police (2007), Tool (2007, 2022), and Bob Dylan (2004).

[39] Currently, Bonnaroo offers a plethora of various artistic, environmental, and community activities throughout the weekend in both Centeroo and Outeroo.

These activities include parades, dance shows, yoga, sustainability lessons, a 5k run, a marriage barn, a water slide, vendor markets, and more.