Designation of protected areas has enjoyed global application as a means of biodiversity conservation for over 100 years. National conservation policy is essential as a means of protecting biodiversity, but is contingent on, amongst others, changing values and international drivers, and remains dynamic in many countries. As conservation policies evolve, the role of pre-existing protected areas within broader strategies for conservation can become unclear, with consequences both for the ability of the conservation policies to achieve their stated goals, and also for biodiversity outcomes within a nation. In order to map evolving inconsistencies between conservation policy and the role of protected areas within it, we develop a conceptual conservation policy framework synthesised from different policy orientations reported in the literature. Using South Africa as a case study, the conceptualisation is used to characterise the policy goals for protected areas in the recently adopted conservation policy, and the pre-existing protected areas system which remains on the statute books. The results indicate that the conceptual conservation policy framework can be used identify misalignment between policy and practice, and has enabled a mismatch to be identified between South Africa’s pre-existing protected areas system and its contemporary conservation policy, which suggests that the management of protected areas is likely to significantly change towards greater access and monetisation at the expense of their intrinsic value.