Makaya Ntshoko was born on October 29, 1939 in Cape Town and grew up in Langa, the township the city built for African residents in the 1920s. His father was a church organist and a strict one, his brother played saxophone, and Ntshoko himself neither drank nor smoked, a discipline his contemporaries remembered as much as his playing. He learned drums from Columbus Phakamile "Phaks" Joya, borrowing Joya's kit until bassist Lami Zokufa talked his father into buying him one of his own, and picked up the rest from trumpeter Banzi Bangani, alto saxophonist Morris Goldberg and drummer Maurice Gawronsky. He worked around Cape Town with altoist "Dan Boy" Danayi and bassist Martin "Lilly" Mgijima and sat in with tenor player Cups Nkanuka's Peninsula Stars. He was also a promising boxer, and the Village Voice's 2017 history of the Jazz Epistles describes him as a former bantamweight prizefighter who chose the drums instead.

In 1959 he went up to Johannesburg with pianist Dollar Brand (who took the name Abdullah Ibrahim in the mid-1970s; the two names belong to one man, and his early credits appear under both) and bassist Johnny Gertze. There they joined Kippie Moeketsi on alto, Jonas Gwangwa on trombone and Hugh Masekela on trumpet to form the Jazz Epistles, a sextet that played no standards at all. Their single album, Jazz Epistle - Verse 1 (Continental CONT 14), was cut at Gallo's Johannesburg studio in a two-day session in January 1960 (some discographies date the session to Sophiatown in September 1959) and pressed in a run of five hundred copies, and it is generally described as the first LP recorded by a Black South African jazz group. Ntshoko also played the February 4, 1960 trio date issued later as Dollar Brand Plays Sphere Jazz (Continental ZB 8047, released 1962), and worked in the pit band of Todd Matshikiza's musical King Kong. After the Sharpeville massacre of March 21, 1960 and the crackdown on public gatherings that followed, the Epistles broke up.

Ntshoko stayed on in South Africa for another two years, co-founding a band called the Jazz Giants (accounts of its lineup differ: the South African critic Gwen Ansell places pianist Tete Mbambisa at its centre, while Wikipedia names Moeketsi, Dudu Pukwana, Gideon Nxumalo and Martin Mgijima) and playing on Nxumalo's Jazz Fantasia, recorded live at the Great Hall of the University of the Witwatersrand in September 1962 with Moeketsi, Pukwana and Mgijima. That concert recording is his last documented South African session. Later in 1962 he left the country, one of the wave of Black South African musicians for whom apartheid had made a working life at home impossible, and he did not live in South Africa again.

He landed in Switzerland, where the Dollar Brand Trio with Gertze took a residency at the Africana club in Zurich from 1963 to 1965 and also played the Atlantis in Basel. Duke Ellington heard the trio in Zurich in February 1963 and took the band to Paris, where on February 23, 1963 he produced two sessions: the trio date released by Reprise as Duke Ellington Presents the Dollar Brand Trio, which includes Thelonious Monk's "Brilliant Corners" (misattributed to Brand on the original sleeve), and a set of ballads with the singer Sathima Bea Benjamin that Ellington shelved and that stayed unreleased until Enja issued it in 1997 as A Morning in Paris. On January 30, 1965 the trio recorded a concert at the Montmartre Jazzhus in Copenhagen, selections from which appeared as Anatomy of a South African Village on Fontana and, from a different part of the same night, as The Dream.

When Brand moved to New York, Ntshoko built a European freelance career out of Copenhagen and then Basel, where he settled and stayed for the rest of his life. In Copenhagen he played the Montmartre behind Dexter Gordon with Kenny Drew and Niels-Henning Ørsted Pedersen (January 6, 1966, issued as Stella by Starlight; September 8, 1969, on Those Were the Days) and behind Brew Moore on February 17, 1966, and he turns up in Storyville's Danish archive series for both Stuff Smith and Ben Webster. He was a regular guest with the Jazz Live Trio in the Zurich radio studio between 1966 and 1969, played the Domicile in Munich on January 11, 1968 in a Benny Bailey sextet with Mal Waldron, Nathan Davis and Jimmy Woode (Soul Eyes), and appeared at the 1969 Ljubljana jazz festival with Dusko Gojkovic's quintet. In January 1972 he recorded Hugh Masekela's double album Home Is Where the Music Is at Island Studios in London with Dudu Pukwana, Larry Willis and Eddie Gomez.

His own band arrived in 1974. Makaya & The Tsotsis, with Heinz Sauer on saxophones, Bob Degen on piano and Isla Eckinger on bass, recorded a single album at SINUS-Studio in Berne on August 6, 1974 for Enja, three of whose five original tracks are credited to all four players jointly. From there he moved easily between the German mainstream-modern circuit and the Swiss free scene: he opened the first Willisau Jazz Festival on August 30, 1975 with John Tchicai and Irène Schweizer (Willi the Pig, pressed in 500 copies), returned to Willisau on October 11, 1975 for the trio date with Joe McPhee and John Snyder that became hat Hut's second release, and recorded with the Anglo-Austrian free group Nicra alongside Nick Evans, Radu Malfatti, Keith Tippett and Buschi Niebergall. For Enja he played Degen's Sequoia Song, Pepper Adams's August 13, 1975 Domicile concert with Walter Norris and George Mraz (released as both Julian and Twelfth & Pingree), Waldron's One-Upmanship with Steve Lacy and Manfred Schoof, Waldron's Moods with Lacy and Terumasa Hino, and Hannibal Marvin Peterson's In Antibes.

He also stayed inside the South African exile network. He recorded Johnny Dyani's Song for Biko on July 18, 1978 with Don Cherry and Dudu Pukwana, played Dyani's Grand Mother's Teaching in 1982, and joined Jazz gegen Apartheid, the band Dyani founded in 1986. Later Swiss work included dates with Johnny Griffin and singer Brigitte Bader in 1989, Stephan Kurmann's string project in 1991, and the Where's Africa Trio with Irène Schweizer and Omri Ziegele, whose Can Walk on Sand was recorded for Intakt in 2009 when Ntshoko was 69. He taught at the music academy in Basel, and in 2007 he came back to South Africa to play the National Jazz Festival at Grahamstown in a Swiss-South African quintet with trumpeter Feya Faku. That same year SteepleChase recorded his second and last album as a leader, Happy House, billed to Makaya Ntshoko & The New Tsotsis, with Andy Scherrer, Vera Kappeler and Kurmann. The Mzantsi Jazz Awards named him a Lifetime Achiever. He passed away in Basel in the early hours of August 27, 2024, at 84, after more than sixty years abroad.

Ntshoko was a busy, polyrhythmic drummer whose playing sat closer to conversation than accompaniment, and German writers have compared his dense cross-rhythms to Elvin Jones's. What made him valuable to so many bandleaders was range: the same drummer swings a Dexter Gordon standards set at the Montmartre, drives the marabi-inflected township themes of the Jazz Epistles and Hugh Masekela's Home Is Where the Music Is, and holds his own in free playing with John Tchicai, Irène Schweizer and Joe McPhee. On his own 1974 Enja album three of the five pieces are credited to the whole quartet rather than to any one writer, which is a fair description of how he worked generally. Mal Waldron, Pepper Adams, Johnny Dyani and Irène Schweizer all called him back repeatedly across two and three decades. Johnny Dyani, who was hard on his peers, singled out Ntshoko and Abdullah Ibrahim as the two who stayed true to themselves and to Africa.