Phosphorus (P) deficiency alters the root morphological and physiological traits of plants. This study investigates how soybean cultivars with varying low‐P tolerance values respond to different P levels in hydroponic culture by assessing alterations in root length, acid phosphatase activity, organic acid exudation, and metabolites in root exudates. Three low‐P‐tolerant cultivars (‘Maetsue,’ ‘Kurotome,’ and ‘Fukuyutaka’) and three low‐P‐sensitive cultivars (‘Ihhon,’ ‘Chizuka,’ and ‘Komuta’) were grown under 0 (P0) and 258 μM P (P8) for 7 and 14 days after transplantation (DAT). Low‐P‐tolerant cultivars increased root length by 31% and 119%, which was lower than the 62% and 144% increases in sensitive cultivars under P0 compared to P8 at 7 and 14 DAT, respectively. Acid phosphatase activity in low‐P‐tolerant cultivars exceeded that in sensitive cultivars by 5.2‐fold and 2.0‐fold at 7 and 14 DAT. Root exudates from each cultivar revealed 177 metabolites, with higher organic acid exudation in low‐P‐tolerant than sensitive cultivars under P0. Low‐P‐tolerant cultivars increased concentrations of specific metabolites (oxalate, GABA, quinate, citrate, AMP, 4‐pyridoxate, and CMP), distinguishing them from low‐P‐sensitive cultivars under P0. The top five metabolomic pathways (purine metabolism, arginine and proline metabolism, TCA cycle, glyoxylate and dicarboxylate metabolism, alanine, aspartate, and glutamate metabolism) were more pronounced in low‐P‐tolerant cultivars at 14 DAT. These findings indicate that increasing root length was not an adaptation strategy under P deficiency; instead, tolerant cultivars exhibit enhanced root physiological traits, including increased acid phosphatase activity, organic acid exudation, specific metabolite release, and accelerated metabolic pathways under P deficiency.