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This study investigated the optimal process of solid-state fermentation (SSF) using soybean meal (SBM) as substrate by Aspergillus oryzaeand proteolysis of SBM to prepare SBM-derived peptide (SBMP) for chelating with Cu(Ⅱ)/Zn(Ⅱ). During the SSF of SBM, the alkaline protease activity of A. oryzaewas higher than that of two other fungi, reaching maximum activity (574 U/g) at the fermentation time of 86 h, 43% inoculation ratio, and liquid–substrate (I/S) ratio of 0.8. The SBMP yield reached a maximum value at 55 °C for 6 h hydrolysis according to the analysis of the degree of hydrolysis (DH) and total Kjeldahl nitrogen (TKN) content in hydrolysates. After ultrafiltration, the SBMP of 1–5 kDa had the best ability to chelate with Cu(Ⅱ) and Zn(Ⅱ). Moreover, the SBMP displayed a higher capacity to chelate with Zn(Ⅱ) (222.7 mg/g) than Cu(Ⅱ) (68.3 mg/g) under optimal conditions. Aspartic acid, glutamic acid, lysine, arginine and histidine in SBMP played a critical role at the chelating Cu(Ⅱ)/Zn(Ⅱ). UV and FTIR spectrum analysis revealed that the –COOH and –NH2in SBMP were the main bioactive groups for chelating with Cu(Ⅱ)/Zn(Ⅱ). SEM showed that the surface of SBMP–Cu(Ⅱ)/Zn(Ⅱ) chelate was rough and formed spherical aggregates. These results indicated that combining SSF and proteolysis exhibited great potential for preparing SBMP–metal chelates for developing organometallic supplements.