Opinions differ as to the importance of organic amendments (OA) for sustaining crop productivity in the intensive, irrigated rice systems of Asia. Our objectives were to (1) quantify the effects of farmyard manure (FYM) and straw incorporation on yield trends in long-term experiments (LTEs) with rice–rice (R–R) (Oryza sativa L.) and rice–wheat (R–W) (Triticum aestivum L.) systems and (2) assess the potential effects of OA on profitability, taking into account long-term effects on yield. We analyzed yield trends in 25 LTE (seven R–R, 18 R–W systems) across a wide geographical range in Asia. Three main conclusions emerged from this analysis. First, application of either manure or straw did not improve grain yield trends in R–R and R–W cropping systems. Second, depending on socio-economic conditions, use of manure or straw in these cropping systems may be profitable, provided these OA are used as a complement to a recommended dose of inorganic NPK (i.e. organic materials should not be used as the primary nutrient source). Third, current experimental designs to assess the suitability of OA need to be improved in order to allow a better comparison of the relative advantages of inorganic and organic fertilizers. The major shortcoming of current designs is that they do not properly adjust mineral fertilizer rates in the inorganic treatments to account for the macronutrient input from OA. Thus, our tentative estimates of the profitability of OA may be overstated.