The System of Rice Intensification (SRI) is a low-input rice (Oryza sativa L.) production system that differs from conventional systems in several ways: seedlings are transplanted earlier and are more widely spaced, organic fertilizer is often used in addition to mineral fertilizer, and soils are irrigated intermittently rather than flooded for long periods. The yield benefits of SRI compared to conventional systems can be substantial, and yet are regionally variable and have been the subject of considerable debate, due partly to a lack of mechanistic understanding. Here we show that soil properties may in part explain the variability in yield response to SRI. A meta-analysis of data from 72 field studies where SRI was compared with conventional systems indicates that yields increased significantly (P<0.0001) when SRI was implemented on highly weathered infertile soils rich in iron and aluminum oxides (Acrisols and Ferralsols), but there was no difference in yield between SRI and conventional systems in more fertile favorable soils for rice production (Gleysols, Luvisols and Fluvisols). The yield difference between SRI and conventional rice production therefore appears to be related in part to soil properties linked to weathering. This should help resolve the debate about the value of SRI and allow research to be targeted toward understanding the biological and chemical processes in soils under SRI management.