Protected areas are increasingly promoted for their capacity to sequester carbon, alongside biodiversity benefits. However, we have limited understanding of whether they are effective at reducing deforestation and degradation, or promoting vegetation growth, and the impact that this has on changes to aboveground woody carbon stocks. Here we present a new satellite radar-based map of vegetation carbon change across southern Africa’s woodlands and combine this with a matching approach to assess the effect of protected areas on carbon dynamics. We show that protection has a positive effect on aboveground carbon, with stocks increasing faster in protected areas (+0.53% per year) compared to comparable lands not under protection (+0.08% per year). The positive effect of protection reflects lower rates of deforestation (−39%) and degradation (−25%), as well as a greater prevalence of vegetation growth (+12%) inside protected lands. Areas under strict protection had similar outcomes to other types of protection after controlling for differences in location, with effect scores instead varying more by country, and the level of threat. These results highlight the potential for protected areas to sequester aboveground carbon, although we caution that in some areas this may have negative impacts on biodiversity, and human wellbeing.