Irrigated rice-based systems in Asia are among the most productive and intensively cultivated agro-ecosystems in the world. These agro-ecosystems with continuous cultivation of rice are characterized by soil submergence before land preparation, tillage with standing water to destroy soil structure, and soil submergence during most or all the period of rice growth. Two or three rice crops are typically grown each year. In some areas of Asia, a rice crop in these systems is being replaced by another crop such as maize in response to limitations in irrigation water and high demand for maize. The conversion from continuous rice to rice–maize cultivation results in increased soil aeration, which can lead to loss of soil organic matter and increased accumulation and loss of soil nitrate. In other areas of Asia, where rice has historically been rotated with other crops such as wheat, the non-rice crop is being replaced by maize in response to increased farm income from maize. The conversion from rice–wheat to rice–maize cultivation can lead to greater extraction and removal of plant nutrients and altered pest and disease dynamics. The food security of Asia depends upon rice-based agro-ecosystems for sustained increases in food and feed production. Increased production must come largely through increased yields because the land area is often shrinking due to conversion to non-agricultural uses and the scope for increased cropping intensity is limited. Managing rice–maize in these agro-ecosystems for high sustained productivity requires tillage, water, and crop residue management to maintain soil organic matter; nutrient management for the production system to achieve high yields with minimal carryover and loss of nitrate and nutrients between crops; and management of pests and diseases within the crop rotation rather than for a single crop.