[1][2][6] However, a little over a year into his tenure, the newspaper announced that he had resigned in order to return to the Sunday Times as editor, a position from which Mathatha Tsedu had recently been fired.

[4] After he had resigned from the paper, the Mail & Guardian named him as one of three journalists who were expected to "emerge as key figures in our public life over the next decade", saying, "Few South African editors enjoy as much respect from their peers and political movers and shakers".

[13][14] In March 2010, it was announced that Ray Hartley would replace Makhanya as Sunday Times editor and that he in turn would become editor-in-chief of all Avusa Media newspapers.

[15] Makhanya remained in the position after Avusa changed ownership and became the Times Media Group, but he resigned in early 2013 to write a book about South African politics.

As a columnist, Makhanya was an outspoken critic of the 1999 Arms Deal[18] and frequently clashed with the government and supporters of former President Thabo Mbeki.

[22] In August 2022, City Press published a particularly energetic column, entitled "Hail the mass murderer", in which Makhanya wrote of Buthelezi:It boggles the mind how a nation that claims to be appalled at South Africa’s high levels of violent crime can celebrate a mass murderer who contributed so much to the culture of violence that prevails today; how a people that is so fixated on the sins of the past can so casually overlook the sins of a man who was responsible for so much of the killing that happened in the name of apartheid...

It is hoped that the pain that still flows in many families and communities that fell victim to Buthelezi and the IFP’s many raids, assassinations and massacres will haunt those who want to sanitise history and salute the mass murderer.

[26] On that occasion, Makhanya had said that he did not dispute that he had written under a pseudonym, but said, "In that article, I wrote about the violence in KwaZulu-Natal, and what they are trying to do now is to turn things around and say that I have murdered a person.