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Abstract: Understanding the effects of alternative farming on soil quality parameters, such as microbial communities, size, activity and soil nutrient content, is of central importance to concepts of sustainability. Combining organic amendments with chemical fertilizer is a promising approach to develop more sustainable fertilization strategies. We investigated the impacts of quantity, type and application time of organic amendments on temporal dynamics of paddy soil microbial biomass, activity, carbon fractions and nutrient status under a long-term field experiment in a rice–rice cropping system. We established treatments with seven fertilization practices characterized by different quantities and application times of green manure (GM), farmyard manure (FYM) and rice straw (RS) in combination with low amount of chemical fertilizers. We further established one treatment with only recommended amount of chemical fertilizer and an unfertilized control. At all sampling times, organic amendments with low amount of chemical fertilizer enhanced microbial biomass, activity and nutrient availability more than recommended amount of chemical fertilization only and an unfertilized control, with higher quantities of FYM resulting in stronger effects than all other organic amendments. The strongest increase of microbial biomass, activity, carbon and nutrient availability was generally found in the treatment with the most diverse resources and highest amount of organic amendments. Principle component analysis indicated that most soil variables measured were correlated to total soil organic C. Regression analysis indicated that the integrated paddy soil properties were closely related to yearly C input and rice yield. Strong temporal dynamics were demonstrated for all soil variables, indicating that we need multiple time sampling strategies to explore the overall influences of fertilization practices on paddy soil. Our results indicate that the development of effective fertilization practices, especially by manipulating the quantity and type of organic amendments, may improve long-term sustainability of paddy soil ecosystems. [Copyright &y& Elsevier]