The study was conducted to evaluate the performance of the popular isoflavone-rich soybean 'agakong' in upland and in drained-paddy fields. Analysis revealed no significant variation in terms of plant height, number of seeds per pod, number of nodes, and 100-seed weight between the two cropping system. Number of pods was significantly higher in paddy field(234.2kg 10a-1) compared to those harvested in the upland field, which was later manifested on the yield where paddy soybeans obtained 278.1kg 10a-1 whereas upland only obtained 179.3kg 10a-1. This observed difference in yield was attributed to the observed higher amount of N in the paddy soil (0.907%) as compared to the upland soil (0.458%). In terms of nutritional content, protein and phytic acid contents were the only parameters that showed significant differences while oil, sugar, reducing power and fatty acids were all comparable in paddy and filed condition. Protein content was higher in upland soil (47.4%) than that of the paddy (44.9%) soil. On the opposite, phytic acid was higher in paddy (2.90%) than in upland (1.09%). This study showed that the yield of soybean is generally a factor of soil N, drained-paddy field production of soybean is comparable to upland-filed production with the benefit of increasing phytic acid content while maintaining its nutritional value.