[3] The shock of this isolation from other branches of the Reformed Churches worldwide led to the adoption in 1986 of the Belhar Confession by some branches of the DRC; the NGK, while stopping short of adopting the Belhar Confession, retracted its 1976 defence of apartheid as a biblical imperative, instead releasing a "more nuanced" document called Church and Society that provided "qualified support for separate development.

"[4] However, the document "reflected the new majority consensus within the NGK which rejected the older, Kuyperian theology"[5] and thus outraged the more conservative clergy within the NGK: as a "direct result"[6] the Afrikaanse Protestantse Kerk was founded in Pretoria on Saturday, 27 June 1987 by 3000 dissidents, together with conservative elements from other branches of the DRC in South Africa.

In 1988 the APK set up a seminary so its pastors could be trained independently, the Afrikaanse Protestantse Akademie, which is based in Pretoria.

[10] The church also holds to the traditional, pre-1986 views of the DRC in that it believes that the Bible not only condones, but actively prescribes, racial segregation.

[12] This belief is traditionally justified on their interpretation of God's commandment to the Israelites in the Old Testament to separate themselves from the heathen nations.