Lonnie Smith was born on July 3, 1942, in Lackawanna, New York, a Buffalo suburb, and was raised by his mother and stepfather. The family had a vocal group and a radio program, and his mother introduced him to gospel, classical music and jazz. He sang in several vocal groups in the 1950s, among them the Teen Kings, whose members included the future saxophonist Grover Washington Jr. and Washington's brother Darryl on drums. A Buffalo music-store owner named Art Kubera gave him his first Hammond B-3 organ, and he learned the instrument from records by Jimmy Smith, Wild Bill Davis and Bill Doggett before he was working Buffalo clubs.

He moved to New York City in 1965 and met the guitarist George Benson, then a member of Jack McDuff's band. The two formed the George Benson Quartet, featuring Smith, in 1966, and made two Columbia albums, It's Uptown and The George Benson Cookbook. Smith's own first album, Finger Lickin' Good Soul Organ (Columbia, 1967), kept Benson on guitar and added the baritone saxophonist Ronnie Cuber, the drummer Marion Booker Jr. and the guitarist Melvin Sparks as a guest. That same year he met the alto saxophonist Lou Donaldson, who took him and Benson into the studio for the Blue Note album Alligator Bogaloo, recorded on April 7, 1967, with the cornetist Melvin Lastie and a drummer credited as Leo Morris, later known as Idris Muhammad. Smith stayed in Donaldson's band for several years and played on Mr. Shing-a-Ling (recorded October 27, 1967) and Everything I Play Is Funky (1970), among other Blue Note dates.

Blue Note signed him as a leader in 1968. Think! (1968) paired his group with Lee Morgan and the tenor saxophonist David "Fathead" Newman, and Turning Point, recorded on January 3, 1969, at Rudy Van Gelder's studio, added Morgan, the tenor saxophonist Bennie Maupin and the trombonist Julian Priester. Move Your Hand was recorded live at the Club Harlem in Atlantic City on August 9, 1969, and its success took his reputation beyond the Northeast. DownBeat named him its top organist in 1969, according to AllMusic. Drives followed in 1970, along with a live date recorded in Detroit on May 21, 1970, with Benson on guitar, that Blue Note shelved until 1995 as Live at Club Mozambique. He left the label that year.

His next stops were Creed Taylor's Kudu label, where Mama Wailer (1971) put him on organ, clavinet and vocals alongside Grover Washington Jr., Ron Carter, Billy Cobham and Airto Moreira, and then the producer Sonny Lester's Groove Merchant and LRC labels. Afro-Desia (1975) used a young Joe Lovano and Carter on electric bass; Keep On Lovin' (1976) found him playing Fender Rhodes with a horn and string section that included Randy Brecker; and Funk Reaction (1977) and Gotcha' (1978) drifted through funk, fusion and even a disco-flavored track. He added "Dr." to his name during these years, a title that was never academic. The 1980s were quieter: When the Night Is Right! (Chiaroscuro, 1980) and Lenox and Seventh (Black & Blue, 1985, with the drummer Alvin Queen), then long stretches spent mostly out of the recording business, living in Hawaii and Florida, according to AllMusic. His records were finding a second audience in the meantime: A Tribe Called Quest sampled his cover of "Spinning Wheel" from Drives in "Can I Kick It?" (1990).

He returned to the studio in 1993 with Afro Blue, a John Coltrane tribute issued under the billing the Lonnie Smith = John Abercrombie Trio and featuring the drummer Marvin "Smitty" Smith, followed by two Jimi Hendrix tribute albums in 1994 and the long-delayed Live at Club Mozambique in 1995. The 2000s were a steady run of club and festival work and albums: The Turbanator (32 Jazz, 2000, from a 1991 recording), Boogaloo to Beck (Scufflin', 2003) and a series for Palmetto that began with Too Damn Hot! (2004) and included Jungle Soul (2006), Rise Up! (2009) and Spiral (2010). He formed his own label, Pilgrimage, and released the live album The Healer (2012) and the octet recording In the Beginning (2013), with the drummer Johnathan Blake. He rejoined Blue Note in March 2015, and with the label's president Don Was producing he made Evolution (released January 29, 2016, with guests Robert Glasper and Lovano), All in My Mind (January 12, 2018, recorded live at the Jazz Standard in New York City to mark his 75th birthday, with the guitarist Jonathan Kreisberg and Blake) and Breathe (March 26, 2021), on which Iggy Pop sings two songs. He was named an NEA Jazz Master in 2017 and was voted the Jazz Journalists Association's organ keyboardist of the year nine times. Smith died of pulmonary fibrosis on September 28, 2021, in Fort Lauderdale, Florida, at the age of 79, six months after Breathe came out.

Smith was a funk-and-soul-rooted Hammond B-3 player with a hard-bop vocabulary, at home in boogaloo grooves, long modal vamps and ballads, and happy to cover anything from Aretha Franklin's "Think" and the Beatles' "Eleanor Rigby" to Beck, Jimi Hendrix and John Coltrane. His mother introduced him to gospel, classical music and jazz, and his organ models were Jimmy Smith, Wild Bill Davis and Bill Doggett. The "Dr." in his billing dates from the 1970s; its origin is unclear, and he described himself as a doctor of music. He said the turban he wore had no religious meaning and that he had worn one since he was young, and he compared it to the headwear of Sun Ra and to Sonny Rollins's mohawk. His Blue Note records of 1968 to 1970 were later sampled widely by hip-hop artists and sought out by DJs and acid-jazz players, and AllMusic calls him one of the forefathers of crossover jazz. He is a different musician from the keyboardist Lonnie Liston Smith and from the organist Johnny "Hammond" Smith.