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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. [ABSTRACT FROM AUTHOR]