A high salt intake may exacerbate menopausal symptoms and substituting for different types of traditionally made kanjang (TMK; soy sauce) may prevent it. This study examined whether substituting salt with lyophilized TMK containing low and high Bacillus and biogenic amines in a high-fat diet might modulate the menopausal symptoms and the energy, glucose, and lipid metabolism in ovariectomized (OVX) rats. They were categorized into salt (Control), TMK with high Bacillus and low biogenic amines (HBLB), TMK with high Bacillus and high biogenic amines (HBHB), TMK with low Bacillus and low biogenic amines (LBLB), and TMK with low Bacillus and high biogenic amines (LBHB). Sham-operated rats consumed the same diet as the Control. HBLB, HBHB, and LBHB prevented increased tail skin temperature compared to the Control. HBHB and HBLB partially inhibited the increased weight gain and abdominal fat mass by reducing the food efficiency without changing the serum 17β-estradiol concentrations. Serum glucose and insulin concentrations and the insulin resistance index by the homeostatic model assessment for insulin resistance showed a positive association for weight gain. HBLB and HBHB decreased the serum malondialdehyde and tumor-necrosis factor-α levels. Hepatic triglyceride storage was lower in all TMK groups than in the Control, while hepatic glycogen accumulation was higher in the HBLB, HBHB, and LBHB groups than in the Control and LBLB groups. Accordingly, the mRNA expression of peroxisome proliferator-activated receptors-γ(PPAR-γ) was higher in the HBLB and HBHB groups compared to the Control, and that of fatty acid synthase was opposite to PPAR-γ expression. However, HBLB and HBHB improved dyslipidemia and insulin resistance compared to the Control, but their improvement did not reach that of the Normal-control. The acetic acid concentrations in the portal vein were lower in the LBLB than in the Control, while the butyric acid contents were higher in the LBHB and HBLB groups than in the Control. HBHB, HBLB, and LBHB elevated Akkermansia and Lactobacillus, and HBLB and LBLB increased Bacteroides and Ruminococcus compared to the Control. Polycyclic aromatic hydrocarbon degradation, bile acid synthesis, and unsaturated fatty acid biosynthesis were significantly higher in the HBLB group than in the Control group. In conclusion, substituting salts to TMK with a high Bacillus content regardless of the bioamine contents partially improved the menopausal symptoms and metabolic disturbance in estrogen-deficient animals.