There is an increasing concern about using limited high-quality protein sources in the aquafeed industry. The alternative solution to this problem is cost-effective plant proteins such as soybean meal (SBM). However, it is better to improve plant protein-containing diets through processing and supplemental amino acids. This study aimed to examine the effects of fermented soybean meal (FSBM) and supplemental methionine and lysine (ML) in diets on growth, digestibility, and body and amino acid composition in Beluga (Huso huso). Two basal diets (490 g fish meal Kg−1) of fish meal (FM) and fish meal with methionine and lysine (FM+ML) were replaced by 40%, 60% and 80% of FSBM and FSBM+ML (FM, FSBM40, FSBM60, FSBM80, FM+ML, FSBM40+ML, FSBM60+ML and FSBM80+ML; 444 g kg−1 crude protein and 19.77 MJ kg−1 gross energy). The diets were fed to triplicate groups of Beluga (394.6 ± 4.3 g) 3 times daily for 56 days. Results showed that Beluga fed 80% FSBM and FSBM+ML had lower growth and feed utilization. Moreover, Beluga fed FSBM+ML performed poorer than those fed FSBM (P < 0.05). No interactions between fermented SBM and ML were observed in apparent digestibility coefficients (ADC) and body proximate composition except for ADC of crude lipid. ADC in Beluga fed 80% were less than other diets. Substitution of FSBM and FSBM+ML in diets significantly reduced dry matter, ash and crude lipid; Crude lipid increased in groups fed FSBM+ML (P < 0.05). FSBM and FSBM+ML in 60% had higher and lower total amino acids in muscle and faeces (P < 0.05), respectively. Also, excreted total amino acids in faeces increased with ML (P < 0.05). Generally, in Beluga, FSBM-containing diets showed better effects on growth, feed utilization, whole-body lipid, and muscle and faecal amino acids than those with FSBM+ML. Fermented SBM could be replaced up to 60%.