Ultra-processing food (UPF) has been a nutrition and health interest. This study is aimed to investigate the association between UPF consumption and the risk of obesity or dyslipidemia.This study is performed using an ongoing cohort study including 17 310 individuals aged ≥40 years in South Korea. UPF is categorized by the NOVA system and FCS, respectively. After an average 5-year follow-up, there is a positive association between NOVA-defined UPF and dyslipidemia. The risk of the Q4 group is almost 20% higher than that of the Q1 group (men, adjusted HR = 1.209 [95% CI 1.039-1.407], women, adjusted HR = 1.195 [95% CI 1.096-1.303]). Consuming high-FCS foods (less processed and healthier foods) show a lower risk for dyslipidemia in both sexes and lower obesity risk in women compared to low-FCS consumption (men, dyslipidemia, adjusted HR = 0.857 [95% CI 0.744-0.988]; women, dyslipidemia, adjusted HR = 0.919 [95% CI 0.850-0.993], obesity, adjusted HR = 0.759 [95% CI 0.628-0.916]).Higher UPF intakes assessed by the NOVA system and FCS are associated with increased incidences of dyslipidemia and obesity. Furthermore, NOVA-defined UPF shows a statistically significant negative association with AMED score, indicating poor diet quality.