Climate change is expected to result in an increase of intra-seasonal rainfall variability, which has arisen from concurrent shifts in rainfall frequency, intensity and seasonality. Changes in intra-seasonal rainfall variability are likely to have important ecological impacts for terrestrial ecosystems, and quantifying these impacts across biomes and large climate gradients is required for a better prediction of ecosystem services and their responses to climate change. Here we use a synthetic weather generator and an advanced vegetation dynamic model (SEIB-DGVM) to virtually conduct a series of "rainfall manipulation experiments" to study how changes in the intra-seasonal rainfall variability affect continent-scale ecosystem responses across Africa. We generated different rainfall scenarios with fixed total annual rainfall but shifts in: (i) frequency vs. intensity, (ii) seasonality vs. frequency, (iii) intensity vs. seasonality. These scenarios were fed into the SEIB-DGVM to investigate changes in biome distributions and ecosystem productivity. We find a loss of ecosystem productivity with increased rainfall frequency and decreased intensity at very low rainfall regimes (<400 mm year<sup>−1</sup>) and low frequency (<0.3 day<sup>−1</sup>); beyond these very dry regimes, most ecosystems benefit from increasing frequency and decreasing intensity, except in the wet tropics (>1800 mm year<sup>−1</sup>) where radiation limitation prevents further productivity gains. This finding reconciles seemingly contradictory findings in previous field studies on the direction of rainfall frequency/intensity impacts on ecosystem productivity. We also find that changes in rainy season length can yield more dramatic ecosystem responses compared with similar percentage changes in rainfall frequency or intensity, with the largest impacts in semi-arid woodlands. This study demonstrates that not all rainfall regimes are ecologically equivalent, and that intra-seasonal rainfall characteristics play a significant role in influencing ecosystem function and structure through controls on ecohydrological processes. Our results also suggest that shifts in rainfall seasonality have potentially large impacts on terrestrial ecosystems, something that should be explicitly examined in future studies of climate impacts.