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The Millennium Ecosystem Assessment identified habitat loss due to the extensive growth of agriculture as the primary driver of biodiversity loss. One implication of this is that agricultural intensification has the potential to reduce threats to wild species. In this paper we consider the evidence for differences in the threat to biodiversity posed by the intensive and extensive growth of agriculture in Sub-Saharan Africa. Using data on numbers of endemic species weighted by overall threat status, we analyze the impact of agricultural productivity growth and agricultural land conversion in 27 countries on threats to mammal, bird and plant species over two time scales: one covering the period since agricultural and environmental records began, the other covering the last decade. We find that the extensive growth of agriculture is associated with increasing threats to biodiversity at all time scales. While intensification is associated with a significant reduction in the threat to all species on long time scales, however, we find that it has no significant effect on shorter time scales.