In the 1990s the New York scene of groove-based jazz was dominated by Medeski, Martin & Wood: keyboardist John Medeski, bassist Chris Wood and drummer Billy Martin, all of them white. The acoustic Notes From the Underground (january 1992), on which Medeski played a grand piano and penned the 13-minute Querencia, achieved an inspired fusion of jazz tradition with funky and hip-hoppish rhythms.

The trio also penned Hermeto's Daydream, The Saint, La Garonne, Uncle Chubb, Rebirth, Otis, besides an eight-minute cover of Wayne Shorter's United and an eight-minute cover of Duke Ellington's Caravan.

But the highlights of the electric and commercial It's a Jungle in Here (august 1993) were Afro-funk and reggae covers. They settled on a compromise on Friday Afternoon In The Universe (july 1994), that was basically an album of old-fashioned soul-jazz with the neurotic accent of the 1990s (The Lover, We're So Happy). They plunged into late-night lounge-music with the languid Shack Man (1996), but resurrected with Farmer's Reserve (february 1997), a set of free improvisations, with Combustication (1998), featuring collaborations with turntablist Jason "DJ Logic" Kibler (Sugar Craft, Start Stop, Church of Logic) as well as acoustic pieces (Latin Shuffle), with the dense soundscape of The Dropper (2000), featuring cellist Jane Scarpantoni and guitarist Marc Ribot, and with the even more abstract Uninvisible (2001), enhanced with horns and turntables.

End of the World Party (2004) and Out Louder (january 2006), a collaboration with guitarist John Scofield, veered again towards a more commercial format.

The trilogy "Radiolarians" consists of Radiolarian I (february 2008), II (july 2008) and III (november 2008).

Together Again - Live At The Egg, (april 2009) documents a session between pianists Lee Shaw and John Medeski with bassist Rich Syracuse and drummer Jeff Siegel.

Live performances by keyboardist John Medeski, guitarist John Scofield, bassist Bill Martin, and drummer Chris Wood were collected on the double-disc In Case The World Changes Its Mind (2006) and on the double-disc Out Louder (2006).

Free Magic (2012) documents their first-ever acoustic tour in 2007.

Billy Martin formed Wicked Knee with Steven Bernstein (trumpets), Curtis Fowlkes (trombone), Marcus Rojas (tuba) and Shelley Hirsch (vocals), documented on the EP Wicked Knee (Amulet, 2011) and on Heels Over Head (2013). Martin also recorded Shimmy (2013), a collaboration with keyboardist Wil Blades.

John Medeski's A Different Time (2013) was a solo piano recording.

The Road To Jajouka (2013) features music by Ornette Coleman and John Zorn (alto saxes), Marc Ribot (banjo), Lee Ranaldo (guitar), John Medeski (Hammond organ), Bill Laswell and Chris Wood (basses), Billy Martin and Mickey Hart (drums) along with the Master Musicians of Jajouka from Morocco.

Medeski, drummer Billy Martin & bassist Chris Wood, and guitarist Nels Cline recorded the live improvisations of Woodstock Sessions 2 (august 2013).

Simulacrum (december 2014), composed by John Zorn, inaugurated an organ trio with Cleric's Matt Hollenberg and Kenny Grohowski.

Mad Skillet (Indirecto, 2018) documents a line-up with Will Bernard (guitar), Kirk Joseph (sousaphone), Terence Higgins (drums), Gilbert Elorreaga (trumpet), Dan Bechdolt (tenor sax), Mark Gonzales (trombone, horn arrangment), Josh Levy (baritone sax) and Jonathan Doyle (bass sax).

Medeski, Martin & Wood performed Omnisphere (february 2015) with the acoustic ensemble Alarm Will Sound, notably Medeski's 20-minute Eye On Ra.

Crawlspace (january 2021) contains two lengthy compositions for "synthesizers, piano and pedals": Movement I and Movement II .