Background The study of body composition and its correlation with lipid profiles are significant markers for the cardiovascular risk factors of the urban Nepali population. This study is an attempt to evaluate the percentage of body fat and determine the parameters that influence the cholesterol levels in the patients attending at Healthy Choice Clinic, Kathmandu, Nepal.Methods A quantitative cross-sectional study was conducted among 106 adult patients of Healthy Choice Clinic aged 18 years and above. Their socio-demographic profile, lifestyle and dietary practice were sourced through structured interview questionnaire. Body Mass Index (BMI), waist-to-hip ratio (WHR), and percentage of body fat were measured through Bioelectrical Impedance Analysis (BIA). For total cholesterol, triglyceride, HDL, LDL and VLDL assessment, blood sample was taken through laboratory tests. Chi-square and fisher’s exact test were used for correlation.Results The statistical prevalence showed that the overweight and obese respondent was 51.9%, and 21.7% obese. In addition, about 86.8% respondents had significant abdominal obesity with high waist to hip ratio (WHR). Of which, alcohol intake significantly correlated with high total cholesterol level among other respondents (p = 0.044). The body mass index (BMl) was significant with total cholesterol level (p = 0.022). The body mass index (BMI), WHR, and body fat percentage were all significantly correlated with high triglycerides (p = 0.019, p = 0.004, p = 0.011; respectively). Regular exercise significantly correlates with reduced very-low-density lipoprotein (VLDL). No significant association was reported between cholesterol and fat percentage and WHR and most of the dietary variables.Conclusions Although we could not find a strong correlation between body fat percentage (BFP) and cholesterol levels, BMI and central obesity indicators can provide valuable correlation with CV risk relating to dyslipidemia. Physical activity is shown to have a protective effect against dyslipidemia. These results can support the significance of a detailed clinical assessment with anthropometric measurements and lifestyle history to identify and manage patients with risk factors for CV disease.