In Japan, health insurers are obliged to conduct Specific Health Checkup (SHC) for middle-aged and elderly persons. High-risk persons are referred to Specific Health Guidance (SHG) to receive behavioral counseling based on individual action plans including targets for modification of daily energy balance through diet and physical activity. Using individual-level observational data, we examined the effects of diet and physical activity counseling on cardiometabolic biomarkers across the country. Subjects were 363,440 high-risk persons aged 40–64 who participated in intensive support in SHG for ≥3 months between April 2008 and March 2012. We considered participants as receiving counseling on diet alone, physical activity alone, combined, or neither if they had targets for diet only, physical activity only, both, or neither, respectively. Biomarkers included body mass index, waist circumference, systolic and diastolic blood pressure, high-density lipoprotein cholesterol, and hemoglobin A1c. Under the difference-in-differences approach, we used multivariable linear regression on repeated measures of biomarkers at SHCs before and after SHG and estimated the effects of each counseling type as an interaction with time of SHC. Compared with neither counseling, diet and physical activity counseling, alone or combined, were significantly associated with additional improvements in biomarkers after SHG, for example, body mass index (men: 0.03–0.06 kg/m2, women: 0.10–0.15 kg/m2) and waist circumference (men: 0.16–0.29 cm, women: 0.43–0.47 cm) in both sexes and high-density lipoprotein cholesterol in men (0.13–0.29 mg/dL). Modest improvements in biomarkers were associated with diet and physical activity counseling, although effect sizes were small.