Despite the permanent takeover of the Cape Colony by the UK in 1806, the church remained semi-established with congregations supported from government funds.

[2] In the 1830s, Boers left the Cape Colony and established republics in the interior of South Africa in what came to be known as the Great Trek.

In 1841 the American missionary Daniel Lindley took over the leadership from Smit who had at that time become very unpopular amongst the Voortrekkers.

A Dutch minister, Dirk Van der Hoff, took over the leadership of the church in the Transvaal in 1853.

Many of the church's ministers or members either died during the conflict or were sent to faraway British colonies as prisoners of war.

Scorched earth tactics implemented by the British in response to the refusal of a number of Boer commandos to surrender led to the destruction of several NHKA churches along with the archival materials stored within.

Most notably, professor Adrianus van Selms who served in the NHKA at University of Pretoria became a prisoner of war in Japan where he wrote numerous theological treatises.

Support for the Apartheid Regime from the NHKA was not uncritically accepted by all, and many dissenters such as professors Adrianus van Selms,[13] Cas Labuschagne, Berend Gemser and Albert Geyser left the church, with some like Geyser being accused of heresy.

[14][15] Other theologians and church leaders who remained within the NHKA and opposed Apartheid were stigmatized and harassed with a slew disciplinary actions.

In 2010, with the eye on the 69th AKV, five ministers of the NHKA (professors Johan Buitendag, Ernest van Eck, Jimmy Loader, Andries van Aarde and Yolanda Dreyer) made a public statement condemning the theological justification of Apartheid.

During the 69th AKV, a majority of the church's ministers and elders voted that the NHKA's support of Apartheid was in contradiction to the Gospel.

The assembly also stated it will do everything in its power to root out homophobia, gay-hate and any other derogatory behaviour against homosexual persons.