Alternative nutrient management options have improved with many synergistic processes of spatial and temporal scale leading to sustained and stabilized productivity due to concerns over the irregular and uneven application of mineral fertilizers. However, understanding the productivity dynamics of biomass and yield in diverse nutrient management and crop rotation intensities is important. This study was conducted during the transitional period with conventional (CONV), integrated (INT), and organic (ORG) nutrient management under four crop diversification intensities in a dry zone of Sri Lanka. Mono-cropped rice (LOW) and a rice-maize rotation (HIGH) were the starting point. After 1 year, the intensity of diversification was increased by adding interseason sunnhemp (rice-sunnhemp-rice; MEDIUM and rice-sunnhemp-maize; VERY HIGH). The INT LOW system during the 1st cycle was very effective. Crop biomass (41%), final grain yield (28%), and rice equivalent yield (36%) increased with the ORG LOW system than at ORG HIGH system. In the 2nd cycle, there was a higher grain yield (54%) and a higher rice equivalent yield (53%) in the ORG HIGH than ORG LOW. The productivity under VERY HIGH rotation was similar in ORG, INT, and CONV towards the end of two-year study. Halving the amount of mineral fertilizers and compensating with organic fertilizers maintains the productivity of existing crops without losing their full reliance on mineral fertilizers. Increasing the diversity from rice mono-cropping to rice-sunnhemp-maize cropping system delivered better synergy by improving overall productivity and grain yields in the organic system. This provides details for new farming system designs combined with ecological and sustainable pathways.