Crop seed phosphorus (P) is primarily stored in the form of phytate, which is generally indigestible by monogastric animals. Low-phytate soybean lines have been developed to solve various problems related to seed phytate. There is little information available on the effects of P fertilization on productivity, physiological characteristics, and seed yield and quality in low-phytate soybeans. To address this knowledge gap, studies were conducted with a low-phytate line and two normal-phytate cultivars from western Japan when grown under high- and low-P fertilization. The whole plant dry weight, leaf photosynthesis, dinitrogen fixation, and nodule dry weight at the flowering stage were higher in the higher P application level, but were not different between the low-phytate line and normal-phytate cultivars. As expected, seed yield was higher in the higher level of P application for all lines. Notably, it was higher in the low-phytate line as compared with the normal-phytate cultivars at both levels of fertilizer P. The total P concentration in the seeds of the low-phytate line was the same as that of the normal-phytate cultivars, but the phytate P concentration in the low-phytate line was about 50% less than that of the normal-phytate cultivars. As a result the molar ratio of phytic acid to Zn, Fe, Mn, and Cu in seed were also significantly lower in the low-phytate line. From these results, it can be concluded that growth after germination, leaf photosynthesis, nitrogen fixation, yield and seed quality were not less in the low-phytate soybean line as compared with two unrelated normal-phytate cultivars currently grown in Japan, and that low-phytate soybeans may improve the bioavailability of microelements.