Soybean (SB) solid residue after oil extraction was investigated in a hydrothermal modification process to provide an eco-friendly solution to SB solid waste disposal for an actual environmental management effort. SB hydrochars (HCs) were derived either by conventional heating hydrothermal treatment (HTT) under intense conditions (200, 250, and 300 °C for 2 h) or by microwave-assisted hydrothermal treatment (MHTT) under mild conditions (160, 190, and 220 °C for 1 h). Physicochemical properties of SB HCs and the transformation of nitrogen (N) and phosphorus (P) functionalities during HTT and MHTT were characterized using several tools. Ultimate and XPS analyses elucidated N transformation, e.g., 5.51 wt % N of raw SB residue decreased to 3.48 and 3.51 wt % after HTT and MHTT, respectively. The P bioavailability of raw SB (3.46 mg/g) was improved after HTT (26.7 mg/g) and MHTT (10.9 mg/g), depicting the practical application of HCs for soil amendment. Atomic H/C and O/C ratios of SB HCs decreased as treatment temperature increased. HCs showed credible higher heating value (HHV; 22.3–25.5 MJ/kg for HTT and 20.5–22.1 MJ/kg for MHTT), higher than various low-rank coals. Besides, energy densification and fuel ratio improved in intense conditions. The thermogravimetric analysis showed HCs possessed better thermal stability. The improved performance of SB HCs indicated that HTT and MHTT provided a green environmental route of SB waste management, valorization, and utilization.