Site-specific nutrient management (SSNM) provides guidelines for effective nitrogen, phosphorus and potassium management to help farmers make better decisions on fertilizer input and output levels in rice production. I evaluated the assumptions underlying the SSNM strategy for rice in the top rice producing countries in the world: India, Indonesia, Philippines, Thailand and Vietnam. Using a generalized quadratic production function, I explored whether major nutrients are substitutes as inputs, and if there are complementarities between inorganic fertilizer and soil organic matter (SOM). I also used non-nested hypothesis framework to contrast the quadratic model against the linear von Liebig model. Results showed that the relationships among major nutrients vary across sites – some inputs are complements, some are substitutes, and some are independent. In addition, I found that the SOM significantly affects the economic returns to nitrogen fertilizer inputs. Accounting for these relationships in the fertilizer recommendation algorithm can make the SSNM strategy more adaptive to farmer’s fields. In areas where soils have limiting organic matter content, fertilizer subsidy or distribution might not be appropriate means to support rice production. Increased rice productivity can be achieved through integrated soil fertility management and adoption of soil conservation technologies.