Background: The Six-Minute Walk Test (6MWT) is a widely used tool for assessing functional capacity in various populations. Metabolic Syndrome (MetS), a cluster of cardiovascular risk factors, is associated with reduced functional capacity and increased risk of cardiovascular disease and type 2 diabetes. However, the factors influencing 6MWT performance in primary care settings among patients with and without MetS remain underexplored, especially in Indonesian populations. Methods: This cross-sectional study was conducted from April to August 2024, using data from the Germas Jantungku registry at 20 primary healthcare centers in Makassar, Indonesia. A total of 134 participants (59 with MetS and 75 without MetS) were recruited through consecutive sampling. Demographic, medical, and clinical data were collected, including anthropometric measurements, blood pressure, and fasting blood samples for glucose and lipid profiling. Participants underwent the 6MWT, and physical activity levels were assessed using the International Physical Activity Questionnaire (IPAQ). Multivariate logistic regression was used to identify factors associated with abnormal 6MWT performance. Estimated VO2 max was calculated using the Nury formula, and subgroup analyses were performed. Results: Participants with MetS were older (55.17 ± 10.86 years vs 51.01 ± 10.19 years, p = 0.024) and had higher waist circumferences, blood pressure, and lower HDL cholesterol levels than those without MetS. The prevalence of diabetes mellitus (52.54% vs 20.00%, p < 0.001) and smoking (22.03% vs 9.33%, p = 0.041) was also significantly higher in the MetS group. Multivariate analysis revealed that age (OR 1.09, 95% CI 1.03-1.16, p = 0.005) and smoking (OR 12.30, 95% CI 1.02-14.85, p = 0.048) were significant predictors of abnormal 6MWT performance. However, MetS status was not independently associated with abnormal 6MWT performance. Although trends toward lower estimated VO2 max were observed in MetS patients across subgroups, these differences were not statistically significant. In smokers with abnormal 6MWT performance, MetS patients had notably lower estimated VO2 max (12.49 ± 5.06 ml/kg/min vs 17.08 ± 2.39 ml/kg/min, p = 0.058). Conclusion: Age and smoking were significant predictors of reduced functional capacity as measured by the 6MWT, while MetS status alone was not. These findings suggest that in primary care populations, the impact of MetS on functional capacity may be modulated by other risk factors such as age and smoking. Comprehensive management strategies addressing multiple risk factors are necessary to improve outcomes in this population.