Irrigated rice (Oryza sativa L.) ecosystems in Asia are among the most productive agricultural system in the world. The cropping patterns in these systems is often becoming more diverse and including non-rice crops such as maize (Zea mays L.). We compared in a 12-year-old experiment in the Philippines the long-term effects of continuous rice-rice cropping and a rice-maize rotation on changes in soil N supplying capacity, N balances, and crop yields. Soil C and N decreased in the rice-maize rotation. Indigenous N supply, as determined from the yield of rice and the N accumulation by mature rice in the absence of N fertilizer, was consistently lower when rice followed maize than rice. Yield of rice with full fertilizer application was not affected by the previous crop. Rotation of rice with maize reduced the soil N supplying capacity, but it did not prevent the attainment of high rice yield with sufficient application of fertilizer N. The rotation of rice with maize rather than rice could however increase the need of rice for fertilizer N to achieve high yield.