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The forests of Central Africa constitute the continent’s largest continuous tract of forest, maintained in part by over 200 protected areas across six countries with varying levels of restriction and enforcement. Despite protection, these Central African forests are subject to a multitude of overlapping proximate and underlying drivers of deforestation and degradation, such as conversion to small-scale agriculture. This pilot study explored whether transboundary protected area complexes featuring mixed resource-use restriction categories are effective in reducing the predicted disturbance risk to intact forests attributed to small-scale agriculture. At two transboundary protected area complex sites in Central Africa, we used Google Earth Engine and a suite of earth observation (EO) data, including a dataset derived using a replicable, open-source methodology stemming from a regional collaboration, to predict the increased risk of deforestation and degradation of intact forests caused by small-scale agriculture. For each complex, we then statistically compared the predicted increased risk between protected and unprotected forests for a stratified random sample of 2 km sites (n = 4000). We found varied effectiveness of protected areas for reducing the predicted risk of deforestation and degradation to intact forests attributed to agriculture by both the site and category of protected areas within the complex. Our early results have implications for sustainable agriculture development, forest conservation, and protected areas management and provide a direction for future research into spatial planning. Spatial planning could optimize the configuration of protected area types within transboundary complexes to achieve both forest conservation and sustainable agricultural production outcomes.