Important Plant Areas (IPAs) are a successful method of identifying priority areas for plant conservation. Assessment of IPAs, however, often relies on criteria related to species, while incorporation of habitats has been less consistent. Using Uganda as a case study, we test the application of the threatened habitat criterion (criterion C). We identified nationally threatened habitats using Red List of Ecosystems criteria and assess, for the first time, how differing application of thresholds under criterion C can influence IPA network outcomes. Eleven threatened habitats were identified, with declines switching from predominantly forest to savanna after the mid-20th century. Significantly, we found current IPA guidance on use of Criterion C needlessly limits the number of sites that qualify as IPAs. The five best sites threshold is reserved for countries where quantitative data is unavailable, however, the application of the relevant thresholds to quantitative data largely generated fewer than five IPAs, comparably limiting conservation opportunities identified. We recommend, therefore, that the five best threshold is available for application on both qualitative and quantitative data. This will bolster the value of IPAs in conserving and restoring threatened and ecologically important habitats under the Kunming-Montreal Global Biodiversity Framework.