Increased drought frequency in many parts of the world, especially in the global South, is expected due to accelerating climate change. We present a bioeconomic model that unpacks the role of soil biodiversity as contributing to both increasing and stabilizing agricultural productivity in low-input rainfed farming systems. The natural insurance value of soil biodiversity mostly depends on farmers’ risk preferences as well as on the frequency of drought events to be insured against. We show that when the probability of drought increases, soil biodiversity conservation can be an optimal ecosystem-based adaptation strategy. However, this is only likely to be the case up to a given drought probability threshold. The natural insurance value of soil biodiversity for climate change adaptation in drought prone rainfed agricultural systems depends on a combination of key hydrological, agronomic and economic parameters.