Pesticide exposure has been implicated as a risk factor for developing a wide range of adverse health issues. Some examples are metabolic syndromes, including diabetes. This study investigated the relationship between current occupational use of pesticides and metabolic and cardiovascular biomarker levels among organic and conventional farmers in Thailand. In total, 436 recruited farmers were divided into two groups: conventional farmers (n = 214) and organic farmers (n = 222). Participants, free of diabetes, were interviewed and submitted to a physical examination. Serum samples were collected for clinical laboratory analyses, i.e., serum glucose and lipid profiles (triglycerides, total cholesterol, high-density lipoproteins, and low-density lipoproteins). Potential risk factors such as smoking, alcohol consumption, and heavy exercise were significantly different between the two groups. There were significant differences in terms of the years of pesticide use, pesticide use at home, sources of drinking water, and distance between the farmers’ homes and farms between the groups. After adjusting for confounders, current conventional farmers had significantly higher abnormal body mass index (BMI), waist circumference, body fat percentage (% body fat), triglyceride, total cholesterol, and low-density lipoprotein values as compared to organic farmers. Conventional farmers had higher risk of many metabolic and cardiovascular risk factors as compared to organic farmers, putting them at higher risk of metabolic diseases in the future.