Glycemic control, including glycemic variability, is important for the prevention of diabetic vascular complications in patients with type 2 diabetes mellitus (T2DM). There was an association between miso soup intake and insulin resistance. However, the relationship between habitual miso consumption and glycemic control, including glycemic variability, in patients with T2DM remains unknown. We defined people without habitual miso consumption if they did not consume miso soup at all in a day. The average, standard deviation (SD), and coefficient of variation (CV), calculated as CV = (SD/average HbA1c) × 100 (%), of hemoglobin (Hb) A1c levels were evaluated. The proportions of habitual miso consumption of male and female were 88.1% and 82.3%, respectively. The average (7.0 [6.4-7.5] vs. 7.3 [6.8-8.4] %, p = 0.009), SD (0.21 [0.12-0.32] vs. 0.37 [0.20-0.72], p = 0.004), and CV (0.03 [0.02-0.04] vs. 0.05 [0.03-0.09], p = 0.005) of HbA1c levels in female with habitual miso consumption were lower than those of female without. Moreover, habitual miso consumption correlated with average (β = -0.251, p = 0.009), SD (β = -0.175, p = 0.016), and CV (β = -0.185, p = 0.022) of HbA1c levels after adjusting for covariates. However, no association between habitual miso consumption and any glycemic parameters was shown among male. This study clarified the association between habitual miso consumption and good glycemic control, including glycemic variability, in female, but not in male.