Recent studies identified that metabolically abnormal non-overweight phenotype is a risk factor for cardiovascular diseases. However, only little is known about risk factors for the progression from metabolically healthy non-overweight (MHNO) to metabolically abnormal phenotype. In this study, we investigated the impact of respiratory function on the progression from MHNO to metabolically abnormal phenotype. In this retrospective cohort study, 8949 (3872 men and 5077 women) individuals with MHNO, who participated in a health-checkup program from 2004 to 2015, were enrolled. Four metabolic factors (high-normal blood pressure or hypertension, impaired fasting glucose or diabetes, hypertriglyceridemia, and low HDL cholesterol concentration) were used to define metabolically healthy (less than two factors) or metabolically abnormal (two or more factors) phenotypes. Respiratory function was measured by spirometry. Over a median 4.0 years of follow-up, 927 participants progressed to metabolically abnormal phenotype. The percentage of FVC for predicted values (HR 0.98, 95% CI 0.93–1.03, p = 0.418) was not associated with the progression to metabolically abnormal phenotype after adjusting for covariates, including age, sex, alcohol consumption, exercise, smoking status, and body mass index, whereas the percentage of FEV1 for predicted values (%FEV1) (HR 0.87, 95% CI 0.84–0.91, p < 0.001) and the FEV1/FVC ratio (HR 0.86, 95% CI 0.78–0.95, p = 0.004) were associated with the progression to metabolically abnormal phenotype. Decrease in respiratory function in terms of %FEV1 and the FEV1/FVC ratio is associated with the progression to metabolically abnormal phenotype in individuals with MHNO. •Ten percent of MHNO progressed to metabolically abnormal (MA) phenotype.•%FEV1 and FEV1/FVC were associated with the progression to MA phenotype.•FVC, %FVC, and FEV1 were not associated with the progression to MA phenotype.