Lipid remodeling in soybean under phosphorus (P)-limitation stress was investigated via lipidomic analysis. Principle component analysis of lipidome data from plants with 4 unfolded trifoliate leaves revealed that each leaf responded to P-limitation stress differently. Upon P limitation, a substantial decrease in phospholipids was observed particularly in the 1st and 2nd trifoliate leaves, while 3rd, and especially 4th, trifoliate leaves showed lipid profiles similar to those from control plants grown under P sufficiency. Under P-limited conditions, non-phosphorus glycoglycerolipid, glucuronosyldiacylglycerol (GlcADG), significantly increased in the 1st and 2nd trifoliate leaves. The levels of some other non-phosphorus glycoglycerolipids, including monogalactosyldiacylglycerol, digalactosyldiacylglycerol, and sulfoquinovosyldiacylglycerol (SQDG), were elevated under P-limited growth conditions, while there were only slight changes in the total levels of these lipid classes upon P limitation. These results indicate that the lipid metabolic pathway in tissues of soybean plants does not uniformly respond to P-limitation stress, where lipid remodeling is very active in older leaves and phosphate appears to be preferentially remobilized to the younger tissues under P-limited conditions.