Plant phenology plays an important role in regulating water, carbon and energy feedbacks between terrestrial ecosystems and the atmosphere. Consequently, leaf phenological shifts are a sensitive indicator of climate change. Despite being one of the most vulnerable regions to climate change, southern Africa’s vegetation phenology has been poorly studied. Using the Enhanced Vegetation Index (EVI) as a proxy for the Fraction of Absorbed Photosynthetically Active Radiation (FAPAR), we applied a systematic change detection approach to assess patterns of leaf phenological change in 21 metrics in the conservation areas of southern Africa. Because ecosystems differ in their phenological activity, we further performed unsupervised clustering of the data to group the study area into 7 regions with similar phenological traits. We found that leaf phenology has changed by at least 1 standard deviation in each of the 21 phenological metrics between 2000-2019. We also show long-term changes in the length of the growing season primarily due to changes in the green-up period and senescence period in each of the 7 regions. Our study reveals severe changes in the functioning of ecosystems of southern Africa with potential impacts on the feedbacks in the biosphere and across trophic levels. The findings of this study could be useful in formulating sustainable conservation strategies.