[3] Prior to the unification of different rugby union governing bodies in South Africa, he represented SARU, playing as a scrum-half, between 1985 and 1991 and was captain of their side between 1988 and 1991.

During his playing career, he was also a teacher at Gelvan Park Primary School in Port Elizabeth, where he worked for fifteen years.

[5] Immediately after retiring, Coetzee joined the coaching team at his former club as an assistant, however, his side finished bottom of the 1997 Currie Cup table.

[14] He became a selector for the national team at the end of 2003 season, after Rudolf Straeuli stood down after being knocked-out at the quarter-finals of the 2003 Rugby World Cup.

In 2011 and 2012, the Stormers finished as the top South African team during the 2011 and 2012 Super Rugby season's, but was knocked out by the Crusaders, 29–10, in the semi-final in 2011 and the Sharks, 26–19, at the same stage in 2012.

This was Coetzee's last game in charge of the Cape Town franchise, announcing in early 2015 he would be stepping down from his role at the Stormers and Western Province at the end of the season.

He guided them to the semi-finals, with victory over Kintetsu Liners 42–10 in the quarter-finals, but was defeated by the eventual champions Panasonic Wild Knights by the same scoreline in the semi's.

Following that loss, the SARU organised a debrief between the Springboks coaching staff and all the Super Rugby franchise' managements.

They later lost to Italy for the first time, 20–18, and a record loss to Wales 27–13, saw South Africa drop to equal worst World Ranking of 6th.

In February 2017, the South African Rugby Union reviewed the Springboks 2016 campaign and the performances of the head coach Allister Coetzee.

His job was deemed under threat due to the poor season, however the SARU backed Coetzee and it was announced that he will remain as the Springboks coach.

The final test was played at Ellis Park Stadium in Johannesburg, a venue in which South Africa has never beaten France in four attempts.

They turned this defeat around, and put in a better performance in against the All Blacks in South Africa, narrowly losing the game 25–24 in Cape Town.

On 2 February 2018, he was sacked by the South African Rugby Union following a run of poor results across his two-year tenure.

In November he helped Namibia win the Stellenbosch Challenge Cup, defeating Kenya and Zimbabwe in a two-round format competition held in South Africa.

In July 2022, Namibia secured qualification for the Rugby World Cup, and later in the year, defeated Canada for the first time, winning 43–37.

During the 2023 Rugby World Cup, Namibia lost all of the games in the group stage, including two record loss to Italy and hosts and France.