Protected areas are the cornerstone on which conservation strategies are often built. Adapting systems of protected areas to rapid global changes is critical to meet the challenge of conservation in biodiversity hotspots. Twenty years ago, Jaffré et al. (Biodivers Conserv 7:109–135, 1998) warned that the system of protected areas in the global biodiversity hotspot of New Caledonia was not adequate to conserve the threatened plant species. Here, we examine changes in major threats to the New Caledonian flora and whether the system of protected areas has been improved to address these threats. While some improvements have been made, many key shortcomings identified by Jaffré et al. (Biodivers Conserv 7:109–135, 1998) have not been addressed and the majority of threatened species remain outside protected area. During the same time, thousands of hectares of vegetation have burned outside and inside protected areas, a hundred new mining concessions were issued and the rate of nickel mining has doubled. Better protection of remaining natural vegetation on ultramafic substrates, which are severely impacted by both mining activities and fires, is urgently needed. Further convergence between research and conservation actions is needed to tackle increasing threats to the unique New Caledonian flora.