The objective of this study was to investigate the current soil properties in lowland paddy fields in Peninsular Malaysia and to assess the long-term changes in the soil fertility status during 50 years after the Green Revolution. Forty paddy fields were selected close to the study sites surveyed in 1965 and grouped based on six physiographic environments: the brackish swamp (including acid sulfate soils), the brackish alluvium, the freshwater swampand the riverine alluvium in the west coast, and the riverine alluvium and the beach ridges interspersed with swales in the east coast. Soil samples from the depth of 0-15 cm were analyzed for the physicochemical properties. Despite similar fertilizer application rates over Peninsular Malaysia, several differences were found in the current soil properties between different physiographic environments, such as 1) higher levels of clay fraction, 1.4 nm minerals, CEC, exchangeable bases and available Si as well as Mg-and Na-rich status in the brackish environments, 2) higher levels of available N in the riverine alluvium environment in the east coast , and 3) the excessive P accumulation in the acid sulfate soils. The long-term changes well appeared in the dramatic increase of P availability and the alleviation of soil acidity. In addition, the composition of exchangeable bases changed toward Ca-rich and Mg-low status. Large reduction in soil organic matter was found in the swamp environments while those in the riverine alluvium environment in the east coast were increased. It could be concluded that despite the successful increase in rice yield after the Green Revolution, the long-term changes in the paddy soil fertility showed positive and negative aspects depending on physiographic environments. Appropriate fertilizer application schemes taking into account different soil characteristics in different physiographic environments should be required to achieve both efficient, sustainable rice production and environmental conservation.

Over 50 years of the Green Revolution since the 1960s, the global population has increased by 2.5 times, cereal production by 3.3 times and the use of N, P and K fertilisers by 9.4, 4.2 and 4.3 times, respectively. Information is still limited, however, on the influence of these impacts on the fertility status of agricultural soils. Here we investigated the influence of the Green Revolution on 142 paddy soils in three tropical Asian countries, that is, Thailand, the Philippines and Malaysia, during the given period by repeated soil sampling in the 1960s and 2010s at or near the same locations. We revealed that the phytoavailablility indices of three macronutrients – N, P and K, that is, available P, exchangeable K and total N, showed 743% (p < 0.01), 12% and 1% increase on average, respectively, while total C showed 9% decline. Comprehensive investigation of overall fertility status by factor analysis using 11 soil parameters suggested that only the factor scores associated with ‘available P status’ increased drastically in all the three countries (p < 0.01) whereas those associated with ‘organic matter and N contents’ and ‘inherent potentiality’ did not exhibit any consistent changes among the countries. In conclusion, intensive soil/fertiliser management systems under the Green Revolution have successfully improved the nutrient status, especially P status, of paddy soils with slight decrease of soil organic matter over the last 50 years, while a large amount of nutrients applied, especially N and K, has been released from soil to the outer environments. Conversion to a high‐efficiency system of external nutrient inputs with organic matter‐conserving strategies is, therefore, urgently required to secure sustainable food production while restoring the environment during the coming decades. Highlights Paddy soils from 142 locations in three tropical Asian countries were repeatedly surveyed in the 1960s and 2010s. Available P increased by 8.4 times, that of exchangeable K and total N showed 12% and 1% increase, while organic matter level showed 9% decline. Factor analysis indicated significant increase of the factor scores for those associated with ‘available P status’. A high‐efficiency system with organic matter‐conserving strategies is to be established for both sustainable food production and restoration of the environment.